Double Lemon Poppy Seed Muffins
Healthy lemon poppy seed muffins made with whole wheat flour and yogurt. These delightful muffins have tons of flavor!
Updated by Kathryne Taylor on August 30, 2024
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.
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 amount of lemon zest 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.
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!
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.
Double Lemon Poppy Seed Muffins
These delightful muffins are 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. Recipe yields 1 dozen muffins.
Ingredients
- ½ cup cane sugar
- 2 medium lemons, preferably organic (you’ll need the zest of both and the juice of one)
- 1 ¾ cups whole wheat pastry flour, white whole wheat flour or regular whole wheat flour
- 2 tablespoons poppy seeds
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon fine salt
- 6 tablespoons unsalted butter, melted and lightly cooled
- 1 cup plain yogurt (plain Greek yogurt works, too)
- 2 large eggs
- 1 teaspoon vanilla extract
- 2 teaspoons turbinado sugar for sprinkling on top (optional)
Instructions
- Preheat oven to 375 degrees Fahrenheit. Line your muffin tin with paper liners, or 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.)
- Combine the sugar and lemon zest in a medium mixing bowl. Use your fingers to rub the zest into the sugar until it is fragrant and pale yellow. Whisk in the flour, poppy seeds, baking powder, baking soda, and salt.
- In a separate, smaller mixing bowl, combine the butter, yogurt, eggs, vanilla and the juice of one of your bald lemons. Whisk until combined.
- 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.
- Divide the batter evenly between the 12 muffin 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 (if using) and wipe off any sugar that lands between the muffin cups.
- 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.
Notes
Recipe adapted from my blueberry lemon muffins, with references to The Fauxmartha and Two Peas and their Pod.
2025 edits: I retested this recipe and lightly tweaked the amounts of poppy seeds, baking soda (for more browning), flour, butter and yogurt.
Nutrition
The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice. See our full nutrition disclosure here.
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).
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!!!
Kate, thank you so much for this recipe! The muffins turned out amazing, I made them with barley flour :) I’d love to know what you think! http://thedessertedgirl.com/2014/09/10/lemon-and-poppy-seed-muffins/
Your muffins are gorgeous! Love those black and white wrappers. Sounds like I need to buy some barley flour!
Thank you so much Kate, that made my day!
These are divine! My little girl loves them and so do I. So happy to have stumbled across your site :-)
Hooray! Glad to hear it. Thank you, Cathryn!
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 :)
Glad to hear it! Thank you for commenting!
Could I substitute the butter with olive oil?
I haven’t tried it myself, but I bet it will work! Please let me know how it goes if you try it.
…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!
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.
Nice save, June! Glad you enjoyed the muffins!
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.
Either one will probably work! I think all whole wheat or half of each would be great.
These were AMAZING!!! Such an easy grab and go breakfast, and so perfectly lemony!
Hooray, thanks Kat!
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!
Your version sound so good! Thanks, Jessica!
Poppy seeds! You got me thinking! I might try and veganize your recipe for my blog some time soon if you don’t mind :)
Sure, please just credit this post when you post your adaptation!
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.
Holly
Holly, I’m so sorry these muffins disappointed you! I don’t think your flour was the problem. I suspect one of your leaveners (the baking powder or baking soda) has probably expired, so you didn’t get the bubbling action you needed. You can test yours to find out: http://www.thekitchn.com/how-to-test-if-baking-soda-or-baking-powder-is-expired-tips-from-the-kitchn-111759
Ur recipe shows black poppy seeds, can I use the white poppy seeds instead?
Hi DJ, I’ve never worked with white poppy seeds but I imagine they would work!
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!!
Thank you, Janice! So glad you both enjoyed these.
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!
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!
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 :-)
Hooray! Thank you, Jane. Your muffins sound really interesting!
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.
Hey Kristin, the smallest lemons will yield about 2 tablespoons juice, whereas the largest lemons could yield up to 4 tablespoons (1/4 cup).
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!
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!
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
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!
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?
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.
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!
Thank you, Anna! I’m so glad they turned out well for you. Thanks for sharing that 5-minute trick!
Any idea if switching out the eggs for Flax Eggs 1:1 will work ok?
Yes, I think so! Another commenter said that worked.
Love Lemon. Added Blueberries (1/2 cup) instead of poppy seeds since I didn’t have any and used less butter. I think I should have stuck with the full amount as they didn’t dome much (and the batter seemed too dry). Still had a lovely lemon flavor. I used the back of a large spoon to blend the zest into the sugar. Yum!
Thanks, Rebekah!
Hi,
My daughter has a diary intolerance. Could you replace the yoghurt with coconut cream and if so, how much? Still 3/4 cup?
Thanks,
Hi Annabelle, I’m sorry for my delayed response. I think it would work, although coconut cream has a much higher fat content than yogurt. Almond milk might even work. Or, a vegan yogurt.
Hi, when you take the lemon zest from the lemon – do you use the micrograter on the entire lemon? So there is ONLY white showing? Just trying to understand technique to make sure I have enough zest! :)
Yep, that’s how I do it!
hi Kate!! I finally made these and everyone absolutely loved them! the only thing is if I wanted a more fluffier texture what would you modify? I added two eggs bUT they were still pretty dense. the only difference was that I used whole wheat flour and not white whole wheat flour. this is such a good go to for breakfast!
Hi Kate – these muffins look great. Any thoughts on adding protein powder (whey or soy) to this recipe or other muffin recipes to add and extra dose of healthiness?
I just made these muffins and I must say – they are delicious! I was a little worried, when after mixing the batter, it was thick – similar to a cookie dough consistency (thanks for your warning about it being thick — it reassured me that I hadn’t screw up in some way!). They turned out terrific, and the crunchy sugar on top complimented them well. I will definitely make them again – thank you very much for the recipe!
Hi kate,
Can you substitute the butter for oil? How do you think they will turn out?
Thank you
yum. just made them. didn’t have butter so used coconut oil and worked well. didn’t know how they would turn out as batter was so thick, i did add 2 tbsp milk. turned out tasty!
Hi I just read the recipe and I have a question.Do you have to use yogurt or is it optional?
It is an essential ingredient.
Hi Kate,
Can these muffins be frozen ?
Yes!
Hi, Kate. I can’t get a hold of poppy seeds at the moment, is there any way to make this recipe without the poppy seeds? I have all the other ingredients and I was hoping I could just make lemon muffins!
Made this! Lemony flavour was great! I put in less sugar (75%) and used an olive oil/coconut oil combination…but wish I didn’t. The lack of butter and kick of sweetness made the muffins a little flat…I think you need more sweetness with all those poppy seeds. Will try them again soon!
Hi Kate,
I made these muffins today for the very first time and they turned out amazing. I used strong brown flour (as I did not have any other healthy flour) and did not use any vanilla but, wow, they came out awesome! Beginners luck? :) I only got into baking a week ago :) I will make them again and again for sure. Thank you for the recipe.
So glad they turned out well! Thanks for letting me know!
How long should they cook for mini muffins?
Sorry, not sure. I just googled mini muffin baking time and it will likely range between 10 to 15 minutes.
Can coconut sugar be used instead of cane sugar?
Made these tonight for my 11-year-old daughter’s breakfast tomorrow morning and *had* to test one to make sure they were edible. So good! I added 1/2 tsp lemon extract for extra lemon and only had one real lemon, so subbed lime zest for one of the lemons (improv by necessity!). Not sure it made a difference, but will definitely try it next time with the zest of two lemons.
Thanks for posting this. Love that they are 100% whole wheat with yogurt.
These were AMAZING!! Best lemon poppyseed anything I’ve ever had. Thanks for the recipe :)
You’re welcome, Natalie! Thanks for the comment.
I just made these double lemon poppy seed muffins. They are the best. I didn’t have plain yogurt so I used lemon yogurt. Thank you!!
Ooh, sounds extra lemon-y.
They were lemony but they were yummy. :)
This dish is really good. I love cooking and you play this recipe.
Your recipes are delicious! My husband needs to cut back on sugar (who doesn’t!) and I find these are the best answers to his breakfast quest.
Question–I am using a bread pan in place of a muffin pan to make the breads/muffins. Is the temp and cooking time the same?
Thanks,
Phyllis
Hi, Phyllis. I’m working on putting up a reference for pan conversions, but in the meantime, here’s a great reference from AllRecipes.
How would these work with almond flour? I eat gluten free.
Hi, Linnie. Nut flours don’t necessarily behave the same way as wheat flours do, so I think it’d be tricky to make that work. Have you tried Bob’s Red Mill GF blend? It’s a 1-1 swap, so you don’t have to worry about conversions. You can click the link above to check out the ingredients. I hope that helps!
I eat gluten free. Would almond flour work? Thank you Kate. Linnie
Have been using this recipe for a couple of years now. Simply delicious- comes out beautiful every time.
They are well loved by my family and friends, even though there is not a lot of sugar, so that’s a win-win for me!
Wonderful! Thanks, Anne!
Loved these. I used half white whole wheat flour, half whole wheat pastry flour. 2 eggs. Xylitol instead of cane sugar (but I did sprinkle turbinado sugar on top).
FYI mine took about 23 minutes and the tops still didn’t get quite as brown as I’d hoped (maybe due to Xylitol instead of sugar?, but the sides and bottoms are beautifully brown and the texture everywhere, but especially inside, is PERFECT.
Such a nice strong lemon flavor, and plenty of poppy seeds. (OK, I probably put in close to 1/3 cup because I spilled some extra into the bowl.)
I thought whole wheat muffins would be boring but I am sold now. Thank you for the recipe!
I’m so glad your version turned out so well, Curtis! Whole wheat doesn’t have to mean boring. ;)
My son cannot have dairy, what can Inuse instead od yogurt?
Hi Kate, I love your muffin recipes. However, my husband likes the bread version instead of muffins. It’s always a challenge to convert the oven temp. and baking time when I turn the recipes into a bread. Could you include a conversion version? Thank you. Phyllis
hey! i was wondering if i can use coconut oil instead of butter! :)
Yes, that’d work!
I like it very much. I’ll do it at my house, I hope it’s good, thanks for sharing the recipe.