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
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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 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.
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
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.
Ingredients
- ½ cup + 1 tablespoon pure cane sugar
- 2 medium lemons, preferably organic (you’ll need the zest of both and the juice of one)
- 1 ½ cups white whole wheat flour or regular whole wheat flour
- ¼ cup poppy seeds
- 1 ½ 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
Instructions
- 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.)
- 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.
- In a separate, smaller mixing bowl, whisk together the butter, yogurt, egg, vanilla and the juice of one of your bald lemons.
- 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 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.
- 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
- 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.
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).
My kids love this recipe, we are dairy intolerant though, so we make them with olive oil not butter and applesauce not yogurt and they are scrumptious.
THat’s great! Thank you for sharing how you were able to adapt this recipe.
I have been on a search for a good and healthy lemon poppyseed muffin recipe and I believe I have found it. Since we are vegan the only substitution I made was using Bob’s Red Mill egg replacer. They came out so fluffy and moist. So yummy will use again.
Thank you for sharing how you made this Fredra!
Hi! Would love to make these but I’m dairy free. Is there a good alternative instead of yoghurt? Would a nut milk work?
Hi Aysha, I haven’t tried, and since this is a baked good, I’m hesitant to offer suggestions that aren’t tested. Maybe vegan yogurt and flax eggs would work?
Mine didn’t turn out : (
I’m not sure what I did wrong. They did not rise and were in the oven probably 30 minutes, at least, and were still doughy in the middle.
I’m sorry to hear that, Diane. Are you sure you added all the ingredients and measurements? Sounds like something was missed. Sorry I can’t be of more help.
I’ve made these muffins about 4 times now and they are by far the best I’ve found. I usually make them as 36 mini muffins and bake them for 10 minutes. Then I freeze them and pop out a few at a time for a perfect treat.
Thank you for reporting back, Marie! I’m happy you love them. These would be fun mini muffins. :)
I made these and loved them! I wanted a really lemony muffin that didn’t have too much sugar and I thought these were great. I had small lemons, so I used the juice from four small ones. They were sooooo good. Definitely making again. Thank you!
You’re welcome, Nicole!
These muffins are just lovely. Not too sweet, not too dry and light. Wonderful recipe to use for my church baking group as well as with a cup of coffee or tea. Thank you!
You’re welcome! I’m happy you loved them.
Do you think it would be possible to use chia seeds instead of poppy seeds? Thank you!
I have’t tried it, so I can’t say for sure.
We baked it and it turned out like hard lemon balls!
1st. I think the recipe only yields around 8 muffins instead of 12. We followed your instruction and ended up with 24 small muffin balls.
2. Texture: very hard. Perhaps with tiny size and baking time was 16 minutes, it overbooked the muffin.
We followed everything as it was written.
A big disappointment for me and my daughter!
I’m sorry this one didn’t turn out for you, Maria. It sounds like there was something that wasn’t measured correctly or the muffin tins were filled too full. How did you measure your flour?
These muffins turned out wonderfully! I had to make some recipe adaptions to make these gluten-free and replace the yogurt with vegan buttermilk since I didn’t have any yogurt on hand. I also made a blueberry-lemon icing which paired very well with the muffins.
For gluten-free: I just used regular GF AP flour, but I added 1/2 tsp xantham gum to the dry mix. In my experience, GF baked goods don’t brown up like regular wheat flour, so mine were still pretty pale at the end but baked through just fine.
For the vegan buttermilk: Mix 3/4 cup dairy-free milk with 3/4 Tbsp apple cider vinegar, then let it sit for 5-10 minutes before adding the other wet ingredients.
For the blueberry-lemon icing: I don’t measure icing because it’s a pretty simple formula: lots of powdered sugar and a little liquid. I’ve found it works just fine to tweak it as you go along. You basically want to start with what looks like an obnoxious amount of powdered sugar, add a tiiiny amount of milk or dairy-free milk (I recommend no more than 1 Tbsp at a time). Mix it together and continue adding milk until it’s half wet, half dry. Then add 1-2 tsp lemon extract or lemon juice and ~2 Tbsp or so of blueberry juice. For the blueberry juice, I microwaved some frozen blueberries, then crushed them up with a fork, then put them in a sieve to squeeze out the juice using the back of a spoon. If your mix gets to be too runny, just add some more powdered sugar.
Thank you for sharing how you adapted this recipe! I know others will find it helpful.
My batter came out very dry! I double checked to make sure I didn’t miss any ingredients. I used plain whole wheat flour and greek yogurt.
Thanks!
Hi Robyn, I’m sorry to hear that. How did you measure the flour? Be sure to spoon and level it.
These were delicious! Thanks for the great recipe.
You’re welcome, Rae!
Can you substitute flax seeds for poppy seeds for toddler friendly?
Hi! I recommend this recipe as written. I don’t know how flax would impact your results. Sorry!
Loved them! This recipe is excellent.
Great to hear, Laura! I appreciate your review.
Can this be adapted to use maple syrup as a sweetener? I love the orange cranberry muffins and want these to be sweetened similarly!
Love this recipe! I make them with gf plain flour and have worked out perfectly every time. Love how light and and fluffy they come out.
As I live alone I tend to freeze the batch and stick one in the microwave for a minute when I need an afternoon sweet treat, taste just as good as fresh!
That’s great to hear, Megan! I’m glad you loved it.
These were great! Our household is sick so we were looking for something that would satisfy our sweet tooth but not set us back. My only suggestion is to perhaps use weight in grams for your recipes. I went easy on the lemon zest and juice since I only had huge lemons and not medium lemons. I went too cautious, but if weights were provided, I could’ve accommodated! Thanks for all your great recipes!
Oh. no! I hope everyone is feeling better, Donna.
I’ve not tried this recipe, but I LOVE your other muffin recipes! I’d like to make this in my MINI-muffin tin (24 mini-muffins). Do you know how to convert this recipe for mini-muffins?
Thanks for your reply!
I can’t wait for you to make it! You will use the same temperature, but cut the time in half. However, keep an eye on them so they don’t get burnt.