Say hello to springy, beautiful lemon poppy seed muffins with a light lemon blueberry glaze! This muffin recipe is guaranteed to brighten your day.
I first shared this recipe years ago after polling my audience on Instagram about what muffin flavor they wanted me to make. SO many people requested lemon poppy seed, and these quickly became one of my most popular spring muffin recipes! They remind me of my childhood and I couldn’t be happier to share them with you.
After testing (and re-testing) these babies about 8 times, I’ve become a LEMON LOVAH FOR LIFE.
Ingredients in healthy lemon poppy seed muffins
These lemon poppy seed muffins are made especially for all my lemon lovers. They’re fluffy, tender, perfectly moist with pops of citrus lemon flavor in every bite. Here’s what you’ll need to make them:
- Flour: you’ll need whole wheat pastry flour to keep these muffins nice and fluffy.
- Honey: these lemon poppy seed muffins are naturally sweetened with honey!
- Yogurt: I love that they’re packed with a little extra protein thanks to yogurt. I recommend vanilla whole milk or 2% yogurt.
- Lemon: you’ll need both fresh lemon juice and zest in the muffin batter and in the glaze.
- Eggs: you’ll also need 2 eggs in this recipe.
- Olive oil: I originally made these muffins with butter, but I found that I actually like olive oil even better! You can, of course, use either.
- Baking staples: don’t forget the baking powder, baking soda, poppy seeds and salt. You’ll also need some almond extract to give the muffins that true lemon poppy seed flavor!
Healthy lemon poppy seed muffins made with yogurt
These muffins also use whole milk greek yogurt to give them their incredible texture and to add a boost of protein. Don’t be afraid of a little fat in your yogurt; I know I used to be, but once I started eating whole milk yogurts my tastebuds started dancing like it was 1999.
- If you don’t have whole milk yogurt, I think you could get away with using low-fat greek yogurt, but the texture may not be the quite the same.
- If you want to make these dairy free, you can use coconut yogurt.
Don’t forget the beautiful glaze
Before you get baking, let’s talk about this lemon blueberry glaze situation: I basically want to drizzle my life with this glaze. It’s light but adds a little something extra to every bite (plus look at that gorgeous color!). The glaze is made with:
- Fresh lemon juice & zest
- Powdered sugar
- Jam of your choice. I like to use blueberry jam, but you could also use strawberry or raspberry; it’s up to you!
Can I make them gluten free?
To make these lemon poppy seed muffins gluten free I think oat flour would work well. Feel free to use chickpea flour or all purpose gluten free flour, too. If you use either of these, you may need to add a few tablespoons more liquid. Please know that I have not tested these to be gluten free, these are only suggestions!
Jazz up your muffins
If you want to make these lemon poppy seed BLUEBERRY muffins, just add ¾ cup blueberries to the batter after mixing the wet and dry ingredients together. YUMMMM.
If you find yourself really loving this recipe, be sure to try out my lemon blueberry paleo bread.
Freeze them for later
Yes, these lemon poppy seed muffins are freezer-friendly! Simply wrap muffins individually in freezer-safe bags or store them in a large freezer bag. When you’re ready to enjoy them, reheat for 30-45 seconds in the microwave or simply thaw them at room temperature. I recommend freezing them without the glaze.
More lemon recipes you might like
- Paleo Lemon Blueberry Bread
- Healthy Lemon Bars
- Lemon Cookies with Lovely Lemon Glaze
- Lemon Poppy Seed Blueberry Baked Oatmeal
- Healthy Lemon Poppy Seed Bread
Get all of our citrus recipes here!
Can’t wait to see you guys make these lemon poppy seed muffins. Don’t forget to tag me on Instagram and share your creations with the hashtag #ambitiouskitchen. I would also love if you left a comment below and rated the recipe.
Ambitious Kitchen
Cookbook
125 Ridiculously Good For You, Sometimes Indulgent, and Absolutely Never Boring Recipes for Every Meal of the Day
The Best Healthy Lemon Poppy Seed Muffins
Ingredients
- Dry ingredients
- 1 ½ cups (170g) whole wheat pastry flour or all purpose flour*
- 2 tablespoons poppy seeds
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ¼ teaspoon salt
- Wet ingredients
- Zest from 2 large lemons (about 2 tablespoons)
- ½ cup (168g) honey
- 2 large eggs, at room temperature
- ½ cup (113g) plain or vanilla greek yogurt (I recommend whole milk or 2% yogurt)
- 3 tablespoons freshly squeezed lemon juice (from 1 large lemon)
- ½ teaspoon almond extract (feel free to skip if you don't have it)
- ⅓ cup (67g) extra-virgin olive oil (or sub melted butter)
- Optional mix-in:
- ¾ cup (113g) fresh blueberries
- For the glaze:
- ½ cup (57g) powdered sugar
- 1 teaspoon lemon zest
- 1 tablespoon low sugar blueberry preserves (or jam of choice)
- 1 to 2 teaspoons fresh lemon juice
Instructions
- Preheat oven to 400 degrees F. Line a 12 cup muffin tin with 9 muffin liners and spray the inside of the liners with nonstick cooking spray. Do not skip spraying them!
- In a medium bowl, whisk together whole wheat pastry flour (or all purpose flour), poppyseeds, baking powder, baking soda, salt. Set aside.
- In a separate large bowl add lemon zest, honey, eggs, yogurt, lemon juice and almond extract. Whisk together until smooth and well combined.
- Gently fold in the dry ingredients until just combined, then slowly stir in the olive oil with a wooden spoon until a smooth batter forms. DO NOT OVERMIX. Fold in your blueberries if using.
- Divide batter evenly between the 9 prepared muffin cups. Bake for 11-15 minutes or until tester comes out clean.
- Once muffins are completely cooled, make the glaze: Add powdered sugar, blueberry jam, lemon juice to a small bowl and stir until well combined. If glaze is too thick, add more lemon juice, a teaspoon at a time, as necessary to thin glaze.
- Dip each muffin into glaze, or spoon a teaspoon or two on top. Transfer to a wire rack with parchment paper underneath and allow glaze to set.
Recipe Notes
Nutrition
Recipe by: Monique Volz // Ambitious Kitchen | Photography by: Eat Love Eats
This post was originally published on April 8th, 2019, and republished with an updated recipe and new photos on May 11th, 2025.
I made these muffins but they came out sunk in the middle. Do you know what may have went wrong? I subbed for wholemeal spelt flour. Also I mixed in all the wet together at the same time, instead of doing the olive oil later (by accident). I didn’t think those changes were enough to make them sink though. I measured the leaveners exactly and they are in date etc. Do you know what might have caused it?
Hi! I haven’t used that flour before, and it is essential to add the olive oil later for proper incorporation. Either (or both) of those variables could’ve caused the sinking!
I love your recipe and I make it at least once a month!!
So happy to hear that!
I just wanted to make lemon poppyseed muffins so I left out the blueberries & the glaze & they turned out delicious! I subbed chia seeds for poppy seeds because that’s what I had on hand.
Perfect! Glad you enjoyed!
These muffins are mostly good. I did use AP flour and olive oil (instead of butter). Loved the spongy light texture. My only issue was finding them to taste quite medicinal, from the lemon and honey. The honey flavor almost overpowers everything else. I love honey but I don’t think it works well as a sweetener here. Very easy to follow recipe but I won’t be making these again.
sorry to hear you didn’t like them. I love honey and lemon. maple syrup is a great alternative!
Hi,
The recipe looks amazing! I don’t get whole wheat pastry flour here, only regular whole wheat flour. Since it can make cakes denser and needs more liquid, how should I adjust the recipe? Should I add more milk/yogurt or reduce the flour?
Thanks in advance!
Hi! I haven’t tested these with whole wheat flour, so I’m not 100% sure how I’d adjust the ratios here.
These were sadly a miss for me! I would consider myself a somewhat-experience home baker, so I had some reservations about the low flour content/wet:dry ratio. I’m not sure how I would tweak the recipe exactly, but the muffins didn’t rise much at all and developed a crispy exterior. They taste fine, but I’d skip this one. I love many of the other recipes Ambitious Kitchen puts out!
Hi! So sorry to hear you had an issue. May I ask if you weighed your ingredients? These are very similar to other recipes I have on the site and the dry and liquid ingredients are accurate. To be sure these are indeed correct and accurate I will retest the muffins this month and report back 🙂
Been on the lookout for a healthy lemon muffin for ages! Couple questions: 1. Poppy seeds aren’t available where I’m from – is chia an okay substitute? Or can I just leave them out? 2. Can I use coconut oil instead of olive oil – will that affect the flavour? Love your blueberry Greek yoghurt muffin which uses coconut oil and since coconut oil is cheaper than olive where I’m from would prefer to use that if possible. 3. Do these muffins need the glaze or can I leave that out? ie is the muffin moist enough on its own to omit it? Trying to make it sugar free so it’s baby friendly.
Hi! Feel free to omit the poppy seeds and use coconut oil. The muffins will still be delicious and moist without the glaze!
Delicious! I made mini muffins and baked for 10 minutes and they were ready, i also used 2 tbsp of honey and didn’t have poppy on hand, so I used chia seeds (but would’ve rather poppy flavor!). There was hardly any sweetness but my toddler loved them and so did I. I might try 1/4 cup next time if we were sharing with more sweet toothed adults.
I’m glad you both loved them! Mini muffins sound great 🙂
Delicious! Do you recommend storing them in the refrigerator or can they be left out in an airtight container?
Feel free to keep them at room temp for a day then I recommend storing them in the fridge!
absolutely love all your recipes!! can i sub maple syrup for honey for babies <1 year?! thx!
That should work!
These turned out so delicious! I made a couple swaps and they were awesome. I subbed chia seeds for poppy seeds, used olive oil instead of butter and you can’t taste it at all. I added lemon extract instead of almond, used maple syrup instead of honey, and 3.75% plain Greek yogurt and then added a splash of vanilla. Cooked for 14 minutes and they are delightful.
Perfect! So glad you loved them!
This is a FAB recipe!
I used GF flour (1 c all-purpose and 1/2 c almond flour), 1/3 c of honey, and vanilla instead of almond extract.
My kiddo cannot stop eating them!
Perfect! So glad these were a hit!
These are delicious! I can’t resist anything lemon! I subbed low-fat sour cream for the yogurt and it worked perfectly. Also, I got a full dozen from this recipe, rather than 9. Baked for 14 minutes. The blueberry sauce is to die for!
So good!!
These turned out delicious! I used nonfat vanilla Greek yogurt. Mine came out to 255 calories each and they’re pretty large!
Perfect! Glad you enjoyed!
Can I turn this into a mini 6in 3 layer cake? If so, how would the portions be?
Hi! That should work using the proportions as written.
Another fabulous AK recipe! I’ve made my way through various one pot meals and entrees and now I’ve moved onto desserts :). These were delicious and super easy to make. I made the recipe as written except subbed the butter for olive oil and used mashed blueberries as I didn’t have any jam or preserves handy. Yummy!
Perfect! I’m glad those swaps worked out well. Hope you keep finding new treats to try here!
Made as directed with the almond extract(can taste it and it complements nicely!). Came back to comment bc these are SO good. Fluffy, perfect flavor and texture. So good. I haven’t made the glaze yet. The website won’t let me give 5 stars but it’s definitely worth 5!! Thank you for a great recipe.
Aw this is awesome! So glad these muffins turned out great for you – appreciate your comment 🙂
These were dry and flavorless for me. The bottoms also burnt.
Oh no! I am so sorry these didn’t turn out for you, did you change anything about the recipe?
For the gluten free curious… I used 1 cup Pamela’s all purpose flour mix and 1/2 cup Bob’s Red Mill Oat Flour and they turned out perfect! I honestly wouldn’t have known they were gluten free – the texture was light and fluffy.
Ahh thank you so much for sharing! Glad these turned out great for you ❤️
This recipe was good but I think the oven temp is too high. At 11 minutes my muffins were nicely browned on top but still raw in the center. I ended up lowering the temp, covering with foil to prevent further browning and baking for 10 more minutes.
Oh no! I am so sorry to hear that. Make sure you are baking them in the middle rack, that might be why it cooked on the outside too quickly.
These turned out awesome! I made gluten and dairy free for my personal allergies. If you use an egg replacement, which I did not, it would make these vegan! Here is what I did:
Subbed King Arthur’s 1:1 gluten free flour
Subbed brown sugar instead of honey (ran out of honey) 1:1 and do not pack the measuring cup
Subbed Silk’s vanilla dairy free greek yogurt
Subbed avocado oil for butter
Right before I put the batter in the tin added 10 TBSP of water
Let them bake for 14 minutes
Just wanted to share as they were fabulous!
Thanks for all these notes, Sarah! SO happy they came out amazing 🙂
I love this recipe! My mom follows a gluten free diet so I made them gluten free with a combo of almond flour and 1:1 gluten free AP flour and added blueberries to the muffin mix! They turned out soooo tasty! I’m making them again soon as they did NOT last long!
So happy that worked well and that you loved them!!
This muffin recipe is absolutely amazing! Delicious and on the plus side healthy, I added fresh blueberries to the batter and skipped the glaze.
So happy they turned out amazing! Love the idea of fresh blueberries in the batter 🙂
These are the best lemon poppyseed muffins I’ve ever made! Always gets lots of compliments too.
I’m so happy you and everyone you share them with love them, Janice! Thank you!
Wonderful! Worked well with oat flour as a one to one sub! Wouldn’t recommend baking with oat flour and blueberries because they come out a big soggy from the heaviness of the fruit.