Double Lemon Poppy Seed Muffins

Double lemon poppy seed muffins (made with whole wheat flour and yogurt)

I’m mad at these muffins. Mad because they took me three tries to get just right yesterday. Mad because the third variation turned out so well that I filled my belly with muffins before I went to bed last night. Fortunately, they’re composed of yogurt (instead of sour cream) and white whole wheat flour (instead of all-purpose flour), so they are more redeeming than your average muffins.

I realize that being mad at an inanimate, edible object is totally ridiculous. It’s like being mad at a puppy who’s been caught nibbling on your favorite pair of shoes. Impossible! They’re just muffins and puppies being their irresistible little selves.

lemon poppy seed muffin batter

Actually, after my leavening issues with the other batches yesterday, I’m downright proud of these muffins. After my lackluster first batch, I doubled the initial amounts of lemon zest and poppy seeds found in typical lemon poppy seed muffins, so these guys are bursting with flavor. No sissy muffins here. I also decided to use white whole wheat flour, which retains all of the nutrients of whole wheat flour but has a lighter flavor and color. That way the lemon could really shine.

Before baking, I opted to sprinkle the tops with turbinado sugar, which produces a sweet, crackling top that complements the texture of the poppy seeds. The finished muffins dome up nicely—not as high as they would if they had less poppy seeds and were made of all-purpose flour—but the resulting texture is rich, almost like pound cake.

muffins sprinkled with turbinado sugar

I learned a few tips for muffin making yesterday that might be of interest to you (source: Diana’s Desserts). First, don’t fill your muffin cups over three-fourths full or you’ll get flat, flying saucer-like tops. For nice rounded tops, grease only the bottom of the cups and halfway up the sides.

I’ve also found that paper liners make for easier clean up, but I much prefer the crisp bottoms that result from baking the muffin batter directly against the pan. Lastly, rubbing the zest into the sugar imparts way more citrus flavor than just whisking the two together. Now you know!

baked lemon poppy seed muffins

Lastly, while I love to use natural liquid sweeteners like honey in my baked goods, honey didn’t work here. I tried reducing the amounts of liquid so I could add one-half cup honey in place of the sugar, but the resulting texture seemed kind of spongy and the muffins didn’t taste sweet enough to delight. Plus, it’s impossible to rub zest into a liquid like honey, so the muffins didn’t taste very lemony. I opted to use organic cane sugar instead of honey for these and I’m pleased with the results. One-half cup sugar divided by twelve muffins really isn’t an amount worth worrying about.

Whole wheat double lemon poppy seed muffins - cookieandkate.comDouble lemon poppy seed muffins with yogurt -

Double Lemon Poppy Seed Muffins
4.9 from 15 reviews
Prep time: 
Cook time: 
Total time: 
Serves: 12
Delightful muffins bursting with lemon flavor and poppy seeds. These healthy muffins are made with whole wheat flour and yogurt. Serve with yogurt for a quick and filling breakfast.
  • ½ cup + 1 tablespoon pure cane sugar
  • 2 medium lemons, preferably organic (you’ll need the zest of both and the juice of one)
  • 1½ cups white whole wheat flour or regular whole wheat flour
  • ¼ cup poppy seeds
  • 1½ teaspoon baking powder
  • ¼ teaspoon baking soda
  • ½ teaspoon fine-grain sea salt
  • 5 tablespoons unsalted butter, melted and cooled
  • ¾ cup plain yogurt (plain Greek yogurt works, too)
  • 1 large egg (update 3/20/14: use 2 eggs for richer and slightly fluffier, more cupcake-like muffins)
  • 1 teaspoon vanilla extract
  • 2 teaspoons turbinado sugar for sprinkling on top
  1. Preheat oven to 375 degrees Fahrenheit. Grease your muffin pan using butter or non-stick cooking spray. (Pro tip: grease only the bottoms and halfway up the cups so your muffin tops don’t flatten out while baking.)
  2. Combine the sugar and lemon zest in a medium mixing bowl. Use your fingers to rub the zest into sugar until the sugar is fragrant and pale yellow throughout. Whisk in the flour, poppy seeds, baking powder, baking soda and salt.
  3. In a separate, smaller mixing bowl, whisk together the butter, yogurt, egg, vanilla and the juice of one of your bald lemons.
  4. Pour the liquid ingredients into the dry ingredients. Use a large spoon to mix the two together. Stir only until the flour is fully incorporated into the liquid.
  5. Divide batter evenly between the 12 muffins cups. The batter will be thick but don’t worry, your muffins will turn out great. The cups should not be more than three-fourths full. Sprinkle the muffins with turbinado sugar and wipe off any sugar that lands between the muffin cups.
  6. Bake for 16 to 19 minutes, until tops are golden and a toothpick inserted in the center of a muffin comes out clean. Let the muffins cool for 5 minutes in the muffin pan, then carefully transfer the muffins to a baking rack to cool completely.
  • Adapted from my blueberry lemon muffins, with references to The Fauxmartha and Two Peas and their Pod.
  • Yields one dozen muffins.
  • Feel free to substitute spelt flour for the white whole wheat flour.
  • For a lighter texture, I think you could substitute ¾ cup whole wheat pastry flour for ¾ cup of the white whole wheat flour.

P.s. For more lemon and poppy seed goodness, try my orange poppy seed pound cake (rich and decadent, made with olive oil and yogurt, feel free to sub lemon for the orange), lemon blueberry muffins and lemon blueberry scones (both are made with yogurt, frozen blueberries work great).


  1. says

    These sound heavenly and just what I need right now. I completely, and I mean /completely/ understand your baking woes. I’ve been suffering with refining a coconut and lemon waffle recipe– three tries so far but with my modifications I’ve made on paper, I’m hoping the fourth time later this week will come out perfect. Baking (when you change things all up at least) can be so very frustrating when things don’t turn out but so delightful when they finally do! Perseverance prevails!

    I see all the blueberry muffin options you have and I’m about to delve in. Blueberries are my all time favorite!

    • says

      Baking is tough! Infuriating, even. I hope your next waffles turn out perfectly. I have a coconut waffle recipe on the blog if you want to check it out. I haven’t had blueberries since summer time. Frozen berries to the rescue!

  2. Marcia says

    I love the look and sound of these, and the idea of doubling up on the lemon and poppy seeds is right up my alley. I always find the chemistry side of cooking so fascinating, and it sounds like you had quite a time in the “lab” :-) On another note, can you reveal the maker of the ticking stripe towel (or napkins?) shown in your pictures? That’s exactly what I’ve been looking for!

    • says

      Hey Marcia, thank you. I snatched up the napkin (it’s a square so it’s a napkin, I think) at a local Kansas City store called Pryde’s for 5 bucks. You might be able to call them and ask them to ship them to you. The name on the label is “DII For the Home”. On the back, it says Design Imports, Seattle. Hope that helps!

  3. says

    Funny, I had some trouble with lemon muffins myself a few days ago. The recipe I used didn’t call for baking soda at all. BIG mistake. Twelve flat, lame muffins. :( The second batch was much better, though, thanks to the baking soda! :)

  4. says

    These really look good. Appreciate your tips as well. There is a visiting cake that I make that you also combine the sugar and lemon zest using your fingers. Have not thought about that method again until you mentioned it. It really does work.

  5. says

    Mmmm lemon poppyseed is my favourite kind of muffin! And I love your healthy take on them. Thank you SO much for sharing that tip about not filling the muffin liners, because flat-top muffins are a huge pet peeve of mine (as are ones that get stuck to the paper liner, but I’ll take that over having to scrub out a muffin tin any day). Pinning now!

    • says

      Oh! Another tip I learned—spray the insides of the paper liners and the muffins won’t stick. Try to just spray the bottoms of the cups, though, so they don’t flatten out on top. Sounds a little tricky but I’m sure it can be done. :)

      • Kristin says

        Or just buy the “If You Care Brand” of muffin liners (available at Whole Foods, Amazon, etc.). They are made from unbleached parchment paper, so nothing sticks. In fact, sometimes the liners practically fall of the muffin by themselves. Plus, they are compostable. I wish I would have read your recipe before stopping at Penzey’s Spices today. I don’t have a full 1/4 cup of poppy seeds and now I am stuck craving your muffins until I have a chance to make it back!

        • says

          Hi Kristin, thanks for the tips! I’ve tried that brand of muffin liners and they work great, although they don’t look good in photographs because they’re always falling off!

  6. says

    White whole wheat flour! I need to look out for that, it sounds wonderful! Love the look of your glorious muffins… I can definitely understand why you would have snaffled three into your mouth before going to bed (blame it on Cookie?!). Lovely recipe Kate. You make the most wonderful redemptive treats! xx

  7. says

    I didn’t know you could get white whole-wheat flour either. I made a pizza with regular whole-wheat flour a while ago and found it really boring, so maybe this knowledge would help here! As for the muffins, I have some poppy seeds that I randomly brought back from my last trip to the UK, so maybe this is the recipe to use them in! Thank you, Kate!

    • says

      White whole wheat flour is great! As far as pizza dough goes, though, no variety of whole wheat flour will bubble up as beautifully as brick oven-baked, all-purpose sourdough. It’s a bummer.

  8. mauraeverything says

    I made these last night – they were delicious – I got 11 muffins vs 12, but that’s ok! In case anyone was curious about calorie count, I put the ingredients into MyFitnessPal recipe tool and they are 140 calories each if you get 12 muffins out of the batter. TOTALLY WORTH IT! The sugar/zest mixture was a magical step in the process.

    • says

      Thanks, Maura! I appreciate you sharing the calorie count. Now I don’t feel so bad for eating so many muffins over the past week. ;)

  9. says

    I could just see myself sinking my teeth into a few of these! Tender crumb against the contrast of crunchy seeds and turbinado sugar–yes please. :)

  10. says

    Healthy baking is hard work. If only it was as easy as subbing things in and out. I give you kudos for sticking with it and coming up with these beauties! I love that crunchy sugary top!

  11. Kristin says

    Kate – Lemon poppyseed muffins are my all-time favorite, but I’ve never baked them at home, and usually settle for a mediocre one at a coffee shop. But I am going on a cross-country ski trip tomorrow in the backcountry, and the weather prediction is for a full-on storm. So I am baking these right now to take as a mid-way treat, which we might definitely need!

    The batter alone is incredible – so lemony and bright. I licked the bowl clean and can’t wait to try one out of the oven.

    Thank you!

  12. says

    My life is sadly bereft of lemon poppy seed muffins at the moment and that needs to change. That step of rubbing zest into sugar makes all the difference doesn’t it? These are a little ray of sunshine on a gloomy February day!

  13. says

    Hi Kate :) These look amazing! I just wanted to know what kind of poppy seeds you use. The ones I get here in India are yellowish-white and they don’t look right! Is there another black variety?

    • says

      Hi Gayatri, that’s an interesting question! The only poppy seeds I know are bluish black. Maybe they come in other colors elsewhere, though. Sesame seeds are yellowish white.

  14. says

    The things we’ll do for a perfect muffin…those these do look worth all that effort! Lemon poppyseed is my favorite muffin flavor and I love that you’ve doubled up on the two most important ingredients!

  15. says

    Oh, I get angry at recipes all the time! And it often happens when I’m baking something… it’s supposed to come out light and fluffy and, instead, has sunken in and is dense. But, this is how these things go sometimes.

    I’m so glad you stuck with the recipe because it really does look like the most wonderful breakfast.

  16. G says

    Hi Kate! Just made these yesterday, following your recipe to the tee and they turned out BEAUTIFULLY. This is going to be a staple recipe of mine for years to come. Thank you, and well done!

  17. Lisa says

    Just pulled these out of the oven and they made me so happy. I forgot that I was out of butter until I’d already started so I used olive oil instead. And I just used regular whole wheat flour so they aren’t the prettiest things. But they taste and smell so good! I’m excited to eat these all week for breakfast…if I don’t eat them all tonight!

  18. Tiffany says

    I stumbled upon your blog and made two of your recipes today, the oat flour pancakes and these muffins. The pancakes were delicious as are the muffins…but mine are a little dense. Did I over stir? I felt like it took awhile to incorporate all the flour with the wet ingredients, so I kept mixing. Any suggestions?

    • says

      Hey Tiffany, I’m sorry I didn’t answer your question sooner. You may have over mixed the muffins a bit. Mine were also a little dense, so the other day, I tried adding an extra egg and preferred those muffins to the one-egg version. The additional egg makes the muffins a little more fluffy and rich. I hope that does the trick for you next time.

  19. Rachel B says

    Just made these- only had 1/2 cup yogurt in the house so added 1/4 cup buttermilk.Wonderful texture, perfect with some jam!

  20. Crystal says

    This was my first time making these muffins and they were delish! I was a little worried at first seeing dough vs batter but they turned out great–and I forgot to add salt. I was also able to make 18 vs 12. Will definitely be baking these again!

    Do you have a recipe for almond poppyseed as well? Thanks.

    • says

      Hey Crystal, glad you enjoyed the muffins! I’ve never come across an almond poppyseed muffin, but I think you could just omit the lemon and add a tiny bit of almond extract. Almond extract has a more potent flavor than vanilla, so a little goes a long way!

  21. says

    I had a major vegan/gf mini brownie baking flop yesterday. But somehow I managed to still eat almost all of them. They tasted great and actually had good texture but they were filled with air pockets and looked horrid, haha. I love ANYthing baked + lemony. I don’t blame you for eating yourself into a lemon muffin coma before bed. :)

  22. Stacey says

    You know you’ve got a great muffin recipe when you forget to add the butter and they still taste great! I look forward to making another batch soon with butter. The extra lemon zest and blending with the sugar really created something special. Nice work.

  23. Traci says

    I’m low on butter so am going to give these a shot using coconut oil. I’ll let you know how they turn out!

  24. Courtney says

    Hey, Kate. I’m so glad you fought for this recipe, because it’s amazing. I was already kind of a fan from your pumpkin bread, and I am totally loving these muffins. I made a batch today using coconut oil instead of butter, and they are sooo good. The coconut oil is subtle, and tastes delicious with the lemon. I used two eggs, and they are the perfect consistency. I had two of those giant organic lemons, so I just used the zest and juice of one (thinking it’d be like two regular lemons). It was plenty lemony, but probably needs a little extra zest next time for the full pop in your recipe. They are the perfect sweetness, too. Mine baked perfect at 18 minutes. Thank you so much for getting mad and creating this masterpiece.

    • says

      Courtney, thank you. I’m delighted that you’re enjoying the recipes. Glad to know that they turn out well with coconut oil, too!

  25. Erin says

    These muffins are pretty good! I was worried that the very thick batter would result in a bread-like texture, but the texture was nice. The lemon flavor is on point and the sweetness is perfect. I substituted chia seed for poppy seeds and my husband couldn’t tell the difference :)

    Thanks for the recipe – I will be making this again!

    • says

      Erin, I’m glad the muffins turned out well! I want to try them with chia seeds once I polish off the last of my poppy seed muffins (they freeze well!).

  26. Cynthia says

    These are delicious! So lemony! I didn’t have any poppy seeds, so I used sliced almonds instead. Still very good, and I’ll use poppy seeds next time.

    I found your blog recently when I was looking for some good ways to use soba noodles. I’ve made several of the recipes, and they have all been great!

  27. Mary cristina says

    Great recipie, thanks! I used chia seeds and flax seeds instead at a half a cup and they are quite hearty now! I can feel OK about giving these to my husband , who is diabetic. I also tried my mini-muffin pan so I can just pop one right in my mouth! Super fun for my little ones as well (they don’t even know they’re eating something healthy!) I had to bake mine for a good 20-23 minutes: maybe that’s because I’m at 7,500′? I’m writing this one down for my collection! Thanks again!

  28. Macy says

    These are definitely scrumptious!! Do you have the calorie count though? Just wondering! And thanks again for the amazing recipe!

  29. Barbara says

    Hi Kate,

    For weeks, I had been searching recipes and food blogs for a healthy lemon muffin. I came upon your blog and thought your combination of ingredients was the healthiest for my purposes. I followed your ingredient list only eliminating the poppy seeds and sugar on top. I combined the sugar and lemon zest in a small food processor to blend it completely. I was careful not to over mix the batter. The muffins baked beautifully. The flavor and texture was flawless.

    This passed the test of my most finicky eater—one of my seven year old twin boys! After the first bite, he proclaimed “YUM!!” Whew! I will be baking these for many years to come and look forward to trying some of your other creations.

    Thank you so much for creating the “perfect” lemon muffin. Bravo!

  30. Lauren says

    Hi Kate,
    I tried your recipe this morning because I liked that it was a healthier recipe. My muffins had a nice texture but looked a little lumpy on the top.
    I found that the lemon flavor was subtle. I prefer a stronger lemon flavor. Would you recommend adding more lemon juice or zest? Thanks!

    • says

      Hmm, not sure about the lumpy top. Since these are made with whole wheat flour, they probably won’t ever have a super smooth, domed top. I’m surprised the muffins don’t have enough lemon flavor for you. They have more than twice the amount of lemon that most lemon muffins have. Did you rub the zest into the sugar as directed? That makes the biggest difference. You could always add more zest, though. Juice doesn’t seem to do much.

  31. Carol Breslin says

    Kate: Sorry, I wrote to you about this recipe through “contact” and then I read your advice on commenting through the actual recipe. I misread white whole wheat flour, and used white flour. In fact, I never heard of whole wheat white flour. It sounds like an oxymoron (is that the right word?) After these muffins failed on me, and I realized my error, I googled whole wheat white flour and now I understand it. So, thanks for leading me to a new food item!!! I am going to try the recipe again, using the correct ingredients. By the way, I searched all my cookbooks and no one had a recipe for lemon muffins. I figured out that they must be difficult. I cannot rate the recipe because I did not follow it properly. Plus I think I took the muff-muffs out of the oven too soon!!!

  32. cubie says

    I made these today. I subbed coconut oil for the butter and milled flaxseed for the eggs. They were awesome! Definitely gonna make them again :)

  33. Ariane says

    …so I just tried the recipe using olive oil instead of butter…turned out very tasty! Highly recommend it as I think it’s now an even healthier recipe. Thanks, Kate!

  34. June says

    My lemon skins were too soft to grate so I used my potatoe peeler to
    remove thin pieces of the skin. Then chopped them up in my little ergo
    blender. The pieces didn’t chop up very small so I dumped the sugar in and blended it for about 2 1/2 minutes and it turned out great. A good way to get lemon zest mixed with the sugarwithout having to use your hands. Necessity is the mother of inventions.
    The muffins turned out great and are super delicious. Thank you.

  35. Daphne says

    I’d like to make these lemon muffins and I can’t get to the store. I have white flour and whole wheat flour at home. Which would you recommend to substitute for the white whole wheat? Thanks.

  36. Jessica says

    I had an excess of organic oranges in need of using so I subbed them for the lemon. I used ww pastry flour and spelt flour. Finally, I subbed coconut sugar for reg sugar. Other than that, followed recipe pretty closely. Delicious. Wonderful crumb. Thank you!

  37. says

    Poppy seeds! You got me thinking! I might try and veganize your recipe for my blog some time soon if you don’t mind :)

  38. says

    I was so excited to make these muffins but they turned out flat and a little wet inside even after baking them for another 10 minutes. I just started milling my own wheat berries and I am wondering if freshly ground flour would cause this to happen? Milling my own flour has certainly been a learning curve! Thanks for any info.


  39. Janice says

    My son LOVES lemon poppy seed muffins. I love whole wheat’s taste and nutritional benefits. Luckily my searching led me to this recipe and WOW am I glad. This is absolutely delicious! I used one egg and plain Greek yogurt. I was worried that the big strands of lemon zest would be too lemony, but not at all. A definite keeper. Thank you!!

  40. Julie T says

    HI! I read other comments in which coconut oil or olive oil for the butter is OK and that sugar can be replaced with coconut sugar – BUT have you ever tried it with oat flour? Would you recommend I add 2 eggs if I do that? Looking forward to your reply!

    By the way – made the banana oat pancakes after trying so many recipes and yours was by far the best. Thank you so much!

    • says

      Hi Julie! So glad you enjoyed my banana pancakes. I honestly don’t have much experience replacing regular flour with oat flour, so I’m really not sure how these would turn out. I can imagine that adding an extra egg or two would be a good idea. If you give them a try, please let me know!

  41. Jane says

    Hey Kate, I just made these with spelt flour and sesame seeds as that’s what I had in the cupboard and they were amazing!! The best muffin recipe I’ve come across in ages so thank you :-)

  42. Kristin says

    Approximately how much juice do you get out of 1 lemon? Trader Joe’s sells little organic lemons, but the lemons at my weekly grocery store are gigantic.

    • says

      Hey Kristin, the smallest lemons will yield about 2 tablespoons juice, whereas the largest lemons could yield up to 4 tablespoons (1/4 cup).

      • Kristin says

        I guess, what I meant was how much juice do you personally get out of the lemon you use? I was trying to gauge how much juice I should be using. My 1 lemon yielded a whopping 1/3 cup of lemon juice. I ended up using the 1/3 cup and they were delicious!

        • says

          Sorry, Kristin, I’m kicking myself for not specifying! I don’t think that a tablespoon or two difference will make or break this recipe, though. I’m pretty sure I used medium-sized lemons here, so I’d guess about 3 to 4 tablespoons. So glad your muffins came out well!

  43. Chana says

    Hi. This look really yummie. I just have a problem. I’m allergic to wheat. And can’t have sugar due to candida problems.
    I was wonder if I can sustitute the wheat for oatmeal flour and instead of sugar use stevia or something . In case you say yes let me know please if I use the same amount of oatmeal flour. Thanks

    • says

      Hi Chana, I’m sorry, I really wish I could give you a definite answer. Those are big adjustments and I’m just not sure how well they would work here. I’m sorry!

  44. Anna says

    Hi Kate! I’ve been following your site here for a bit, and I’ve just gotten obsessed with baking, especially muffins. Nothing like a warm, citrus-y muffin on a cool morning! I’m planning on baking these for my grandmother’s birthday tomorrow. I was curious – if I used two eggs instead of one, and replaced half the sugar with 1/4 cup of honey, would they “cancel out?” You mentioned the honey makes the the muffin denser, but the extra egg adds fluffiness. What do you think, or do I sound naive?

    • says

      Hey Anna! Great to hear from you. I wish I knew exactly how the muffins would turn out with those substitutions. Two eggs are definitely a good idea. Not sure about the honey—any time you’re adding liquid, you will probably need to reduce the amount of moisture elsewhere (unless you’re only adding a little bit). Also, honey browns quickly at temperatures above 325 degrees Fahrenheit, so you might end up with some pretty brown muffins unless you reduce the oven temp (which would require more time in the oven, although I’m not sure quite how much). This is why I’m not a baker! :) Good luck.

      • Anna says

        Well, I didn’t use honey but reduced the sugar to 1/3 of a cup and cranked up the oven temperature to 385, baking for about 20 minutes. I followed your tips concerning the 3/4 filling and buttering/greasing only halfway up the sides; the muffins came out beautifully with exquisite and large cracked domes. But I also, after turning off the oven when the muffins were done, let them sit for about five minutes with the oven door cracked open, and then took them out to cool completely. I’m sure that helped with the dome. Lemony, delicious, and full of flavor! Definitely a keeper!

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