Healthy Lemon Poppy Seed Muffins Recipe (V, GF): wonderfully moist and fluffy vegan lemon muffins bursting with poppy seeds and lemon flavor. These gluten free lemon poppy seed muffins are the perfect balance of sweet and tart! Vegan, Gluten-Free, Dairy-Free.
Good morning! It might not be morning in your part of the world right now, but I can basically promise that a good morning is in your future.
Nope, I didn’t suddenly develop psychic powers (which would be equally cool and terrifying all at once), I just… FINALLY cracked my ultimate Healthy Lemon Poppy Seed Muffins recipe!! Yep, it’s time for you to prepare for the best mornings EVER with these fresh-baked citrus delights. 🙂 Update: I recently shared an Easy Vegan Lemon Almond Poppy Seed Bread Recipe that you’ll love!
For a long, long time, my strongest baking points have relied on the Beaming Baker Basics: peanut butter, oats, chocolate and coconut. You love them, I love them, but what about, ya know… all the other stuff.
Aka: the FRUIT.
Aka, more specifically: LEMONS.
There’s nary a trace of lemons on the blog and that’s been fine for me. Ish. So many of you have been requesting lemon recipes, and I thought since the summer is approaching… and Spring finally for realsies is here, that it was finally time to share a lemon recipe.
And guess what vegan + gluten free lemon recipe I decided to share? 😉 Healthy Lemon Poppy Seed Muffins!! Woohoo! More below…
Healthy Lemon Poppy Seed Muffins
Make that moist, soft, and the perfect balance between fluffy and dense healthy lemon poppy seed muffins. These vegan lemon poppy seed muffins are the BEST! Guys, biting into these muffins are like biting into a basket of sunshine. Which sounds pretty bizarre and a tad risky with unexpected consequences, but you know what I mean!
I’ve been working on a basic muffin batter for awhile now… and cataloging, learning and taste testing everything I could find: from store-bought muffins to these muffin recipes:
- Gluten Free Vegan Easy Dark Chocolate Muffins
- Moist Banana Chocolate Chip Muffins
- Gluten Free Maple Pecan Pumpkin Muffins
- Healthy Blueberry Banana Muffins
- Gluten Free Banana Oat Muffins
As you can see from that list, I really, truly had a hard time leaving chocolate out of this recipe… but where would chocolate go into a healthy Gluten Free Lemon Poppy Seed Muffins Recipe anyway? (Don’t worry, I’ll still put some on a tiny chocolate-designated only plate on the side).
Anyway, the best parts of those muffins all got put into here, minus the pumpkin, banana, cocoa, blueberry… dang it. Alright, a lot of those parts where left out, but the basic reader-approved muffin batter elements remained.
Vegan Lemon Poppy Seed Muffins (Healthy!)
These healthy lemon poppy seed muffins are just the right amount of moist. You know what I mean—not too moist that they seem unbaked (which is ONLY cool when it comes to ultimate fudgy paleo vegan brownies and gluten free vegan brownies); and not too dry that they’re, well… dry.
These vegan lemon poppy seed muffins are just the right amount of fluffy—not too cake-like and not too dense–like what Erik and I joke as being the “artisanal bread” texture (i.e. hard as a freaking rock). Did I spell artisanal right??
Best of all, these gluten free lemon poppy seed muffins are bursting with just the right amount of lemon. Lemon juice is mixed right into the wet ingredients and lemon zest makes a snazzy appearance in the batter.
Long story short, which I know we totally passed ages ago, you’ve got to try these! My mom thinks these lemon poppy seed muffins (healthy!! woohoo!!) taste like donuts and my sister Jenny didn’t stop long enough while eating two of these vegan lemon muffins, one after another, to tell me anything negative. Woohoo!!! 😉
TLDR: Gluten Free Lemon Poppy Seed Muffins
If you’re not convinced yet, let me tell you all about these Healthy Lemon Poppy Seed Muffins. They’re:
- made in just two bowls
- (okay, unless you use another for the glaze)
- vegan, gluten-free, dairy-free (my favorite gluten free lemon muffin!)
- delightfully moist, and wonderfully fluffy
- sooooooo goshdarn pretty with perfectly round, domed tops
- just the vegan lemon poppy seed muffin you’ve been looking for
- made with the healthy, whole ingredients you know and love
- seriously taste like a bite of sunshine! (Alright, who even knows what that’s supposed to taste like)
Grab your shiniest, peppiest lemons and meet me in the kitchen! I’m so excited to hear what you think of these gluten free vegan lemon poppy seed muffins! As always, it’s so wonderful experiencing these kitchen adventures with you. I truly appreciate your feedback, photos on IG and emails.
Sending you all my love and maybe even a dove, xo Demeter ❤
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Did you make this gluten free lemon poppy seed muffins recipe? Take a pic and share it on Instagram with the hashtag #beamingbaker and tag @beamingbaker. I would love to see it!
More Recipe Like Vegan Lemon Poppy Seed Muffins
- Healthy Lemon Raspberry Muffins Recipe
- Vegan Soft Baked Lemon Donuts with Lemon Glaze! (Gluten Free)
- Lemon Coconut Macaroons Recipe
- Healthy Lemon Raspberry Muffins Recipe
- Easy Vegan Lemon Almond Poppy Seed Bread Recipe

Healthy Lemon Poppy Seed Muffins Recipe (Vegan, Gluten Free, Dairy-Free)
- Prep Time: 25 mins
- Cook Time: 20 mins
- Total Time: 45 minutes
- Yield: 10-12 muffins 1x
Description
Healthy Lemon Poppy Seed Muffins Recipe (V, GF): wonderfully moist and fluffy muffins bursting with poppy seeds and lemon flavor. The perfect balance of sweet and tart! Vegan, Gluten-Free, Dairy-Free.
Ingredients
Dry Ingredients
- 2 ¼ cups gluten free oat flour – if using homemade oat flour, make sure it’s very finely ground (not coarse)*
- ½ cup finely ground, blanched almond flour
- 1 teaspoon baking soda
- ½ teaspoon baking powder
- ¼ teaspoon salt
- 1 ½ tablespoons poppy seeds
Wet Ingredients
- ½ cup + 2 tablespoons water
- ½ cup non-dairy milk
- 2 tablespoons lemon juice
- zest of 1 lemon (2 tablespoons)
- 3 tablespoons melted coconut oil
- ¼ cup coconut sugar
- ¼ cup pure maple syrup
- ½ teaspoon vanilla extract
Optional Glaze
- 3 tablespoons organic, unrefined confectioners’ sugar** (sugar-free substitute in notes)
- 1 teaspoon lemon juice
Instructions
- Preheat the oven to 350°F. Line a 12-cup muffin pan with cupcake liners. Set aside.
- In a large bowl, sift together all the dry ingredients except salt and poppy seeds: oat flour, almond flour, baking soda, and baking powder. Whisk in salt and poppy seeds.
- Add water and milk to a microwave-safe bowl. Heat in 10-second increments until just warm. This will prevent the melted coconut oil from solidifying once mixed with these liquids.
- In a medium bowl, whisk together all wet ingredients: water, milk, lemon juice, lemon zest, oil, sugar, maple syrup and vanilla. Whisk until well incorporated.
- Add wet ingredients to dry ingredients. Whisk until just incorporated, making sure no flour patches remain.
- Pour batter evenly into prepared muffin pan—filling each cup all the way to the top for big, round tops, and ¾ of the way for a larger quantity of smaller muffins. Bake for 16-22 minutes. Mine took 20 minutes. Insert a toothpick to check for doneness—once it comes out clean, it’s done.
- Place muffin pan on a cooling rack to cool for 20 minutes. Remove muffins from muffin pan and transfer to a cooling rack to cool completely, about 1-3 hours. Optionally, in a small bowl, whisk together Glaze ingredients until thickened: confectioners’ sugar and lemon juice. Drizzle muffins. Enjoy! Storing instructions below.
Notes
*If using homemade oat flour, make sure to sift the flour to remove coarse bits of oats that could create grainy muffins.
**Powdered sugar substitutes: Swerve is a good sugar-free, low carb substitute. You can also grind the sweetener of your choice, such as Xylitol, in a coffee grinder or small blender until you get a powder. Since Swerve is a bit drier, use about 2 ½ teaspoons lemon juice to make the glaze.
**You can also add more powdered sugar if you’d like a thicker glaze.
Storage notes: Store in an airtight container for up to 1 week in the refrigerator, or in a cool, dark environment. Glaze when ready to eat, or day of.
To Freeze: store in an airtight container or bag, unglazed, in the freezer for up to 1-2 months. Allow to thaw for about 30 minutes at room temperature before enjoying. Or, heat in the microwave in 15 second increments until just warm.
- Category: Breakfast, Muffins, Vegan, Gluten-Free, Dairy-Free, Whole Grain
- Method: Bake
- Cuisine: American
Keywords: healthy lemon poppy seed muffins, vegan lemon muffins, gluten free muffins
© beamingbaker.com. All content and images are protected by copyright. Please do not use my images or recipe without my permission. Please do not republish this recipe, instead, include a link to this post for the recipe.
Best Tools for Lemon Poppy Seed Muffins (Healthy!)
Citrus Zester | Muffin Pans (2pk) | Parchment Cupcake Liners | Citrus Squeezer | OXO Trigger Ice Cream Scoop | Gluten Free Rolled oats | Maple Syrup | Coconut Sugar | Coconut Oil | Organic Unrefined Confectioners’ SugarThis post may contain affiliate links, which allow me to make a small commission for my referral, at no additional cost to you. Thank you for supporting Beaming Baker.
I made these muffins this morning and replaced 2 tablespoons of water for 2 more tablespoons of lemon juice. I still wanted a more intense lemon flavor and so I am going to try it with a half a cup of lemon to replace the water. I also want to try using date syrup or sugar since it has fiber and is healthier. I forgo the frosting for I don’t need the extra sugar. I’m might try adding an egg to get better height since I’m not vegan. I’ll let you know how my tweets work.
Sounds great Anona! Can’t wait to hear how it all goes! 🙂
Love the texture of these muffins..and lemon is so irresistible! I’ll try this with home made oat flour. Thank you for the tips!
★★★★★
Oh yes, the texture is fantastic! 😊 Hope you enjoy them Shinta!
I loved having all of the ingredients to makes these muffins! They were a hit!
★★★★★
Woohoo! Isn’t it the best when that happens? 😊 So happy to hear they were a success Suzy!
I love baking with oat flour! Can’t wait to make these!
★★★★★
Same here! 🙂 Happy baking Mary!
These were super moist and flavorful! I loved the poppy seeds with the lemon; a perfect combination!
★★★★★
Ooh I know, it really hits the spot! 😋
I made these muffins for breakfast this morning and they were SO delicious! I loved the bright and fresh flavor!
★★★★★
Woohoo! I’m so thrilled to hear it Jessica! 😄
Could I substitute pecan meal for the almond meal? Our friends own a pecan orchard & I’d like to try it with their pecan meal.
Hi LeAnn! Oh how exciting! I haven’t tried it myself, but I think that should work. Let me know how it turns out!
Hello just finished up glazing my muffins, they look good hoping they taste good too! I made them to bring to work for my birthday treats! Thanks for sharing your recipe, I’ll let you know what they think.
This recipe is a keeper!! They were so moist, lemony, and delicious! And the ladies at work said they were amazing! Thanks again!
Woohoo!!! I just love that you came back to let me know. 🙂 I was waiting on pins and needles! 😉 I’m so pleased that you & your coworkers enjoyed my recipe. Happy baking, Sandee! 🙂
Hello! These look delicious! Can I use a gluten-free flour blend instead of the oat flour? Also, can you suggest any substitutions for the almond meal?
Hi Wren! Yep, you can definitely use a GF blend. As for the almond meal, you could use cashew meal or sunflowers seed meal, or use about 1-2 tablespoons less of GF all purpose flour. Happy baking!
Hi, I am dying to make this recipe. Can I use normal oats if I am not allergic to gluten? or what about steel cut oats from red mills is there any difference? I can’t find the old fashioned rolled oats in my country.
Hi Elena! Yep, if you don’t have a gluten allergy then you can definitely use regular oats to make your own oat flour. Happy baking! 🙂
Hi, I was wondering if you can use almond meal instead of almond flour. Thanks!
Hi Sherry! Yep, that should work fine. Hope you enjoy! 🙂
Hello Demeter! I am so happy to find your site. I would like to ask if I can substitute honey for the maple syrup. May I also ask why you prefer to use maple in your recipes rather than honey?
Hope to hear from you soon 🙂
Judy
Hi Judy! I’m so glad to have you here. . I haven’t tried swapping the maple syrup for honey in this, so let me know how it goes! As for why I use maple syrup, it’s because it’s a wonderful vegan sweetener option. Hope this helps! 🙂
How many calories is in each one give or take?
★★★★★
I can’t believe how yummy these muffins are! Who knew that vegan gluten free baking could taste soooo good! No need for butter and eggs here : )
★★★★★
Oh yeah! ☺️ So happy to hear you enjoy the recipe Chris! Thanks for stopping by to let me know!
The kids will love these, perfect for making over the school holidays
Fantastic! Hope y’all enjoy. 🙂
Hello! Just curious about the reason for 1/2 c water and 1/2 c non-dairy milk instead of a full cup of non-dairy milk. Non-dairy milk is very close to the consistency of water. Thanks for the info!
HI, with what can I sub the coconut sugar with? I don’t have any at home… and I really want to bake them TONIGHT!!
Appreciate it, thanks!
Hi Rene! Did you get a chance to make these yet? Try organic brown sugar. 🙂
These look so good!
Do you think it would work if I omitted the almond flour and just used all oat flour?
Hi Marisa! Yes, but it will turn out a bit drier. I would recommend replacing the 1/2 cup of almond flout with 1/4 cup oat flour. Happy baking!
I’m just making these now cause I adore any lemon flavoured baking! (and cause my family and I are addicted to your chocolate chip banana muffins )
Would it work to add a few blueberries to each muffin? Or would that mess up the batter?
I’m so happy that you and the fam enjoy the muffins Lisa! ☺️ Yep, you should be able to add in some blueberries no problem. Let me know how they turn out!
How could I make this oil free?
They look sooooo good
Hi Unity! You might be able to substitute the oil with applesauce or vegan yogurt—you might need to reduce the wet ingredients just a bit since those two subs are very moist. I’m not 100% sure since I haven’t tried it. Good luck & let me know how it turns out. 🙂
Hi…I cannot eat oat flour. What flour(s) could I use as a substitute? Thanks!
Hi Sheryl, try using gluten free all purpose flour. That should work. 🙂 Let me know how they turn out!
just made these!!! have been wanting these since I went vegan and they taste amazing ! thank u
★★★★★
Woohoo!!! So happy to hear you enjoyed them, Lily. 🙂 Thank YOU for letting me know! .
These are exactly what I’ve been looking for! Your recipes have been a life saver since having to give up gluten,eggs and dairy! Thank you!
★★★★★
Fantastic! I’m so happy that you’ve enjoyed my recipes so much. Big hugs! .
Oh my, these muffins look incredibly good! I wouldn’t mind a deliciously healthy lemon muffin for breakfast – in fact, gimme the whole batch! 🙂 Hope you have a great week, Demeter! xo
★★★★★
Thanks Marsha! The lemony zest is such an incredible treat and moodbooster in the morning! 🙂 Hope you have a great one too, Marsha! xoxo
These are perfect day starter! I am sure my family will love this!
★★★★★
Thanks Sandra! I can’t wait to hear what y’all think! 🙂
That is my kind of breakfast muffins!
Glad to hear it! Hope you enjoy. 🙂
I love love love poppyseed and lemon in anything, so I know these must be delicious!
★★★★★
The combo is so yummy and refreshing! Hope you get to try. 🙂
These look so fun and tasty! I’m loving the looks of these!
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Yeah!! Thanks Erin!
These are perfect for spring!
Yes, absolutely! Thanks Delaney!
Lemon Love!!!!! I’ll raid my Mom’s lemon tree very soon to make a batch. The last bunch I had I actually used a mandolin to make thin round slices and dried them in a food dehydrator. They are like “natural sour patch kids”. I also
break them up and mix in to my fruit salads etc. It’s makes for some serious zinginess to the fruits. If you have a dehydrator it’s super easy and fun. Thanks again for another winning vegan dessert!
Oh yay!!! So amazing that your mom has a lemon tree. .. I am completely astounded and impressed by your natural sour patch kids idea! 🙂 Thank you, Heidi, for leaving yet another wonderful comment. Hope you enjoy!
Hello! Any suggestions for what to replace coconut oil? I’m sensitive to coconut and would love to be able to make these!
Hi Christin, you can replace the coconut oil with dairy-free spread (vegan butter), or perhaps your favorite baking oil. Just remember that the flavor of the oil might affect the final results. Enjoy! 🙂
These muffins look incredibly moist and delicious. I also love anything baked with poppy seeds. I can’t wait to try your recipe!
Thanks Renee! Poppy seeds add such a delicious, spicy kick. Can’t wait to hear your thoughts. 😉
Would certainly be a sunshiny start to the day. These look amazing!
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Oh yes!! Thanks Jules! Wishing you a sunshiny start to the day. 🙂
These sounds perfect! Love the glaze on top!
Thanks Jamielyn! The glaze just makes them SO yummy!
YUM! My daughter LOVES lemon poppyseed muffins and she is drooling over my shoulder over these, Demeter!These would definitely make for the “best mornings ever”! 🙂
Oh perfect! Then I know you two will just love these! Wishing you two the best mornings ever. 🙂
I love everything with lemon and poppyseeds. Just last night I made some poppyseed pancakes for breakfast this morning, and I know that the combination is really good.
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Yes! The combo is unbeatable–especially in the springtime. 🙂 Hope you get to try!
I have a hard time leaving behind chocolate too but I’m thinking I could for one of these muffins. They do look amazingly moist – which I don’t always associate with vegan baking. Great recipe!
★★★★★
Hehe. Right?!? 😉 But yes, you totally do not miss the chocolate in these! 😉 Thank you for the compliment! They’re perfectly moist and so enjoyable!
These muffins will DEFINITELY result in a good morning. Love this recipe!
★★★★★
Oh YEAH!!! Thanks Alida! 🙂
I love lemon recipes. I’ve got this huge drawer full of fresh lemons that I’m so excited to use. These looks great!
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They’re so refreshing and fun! 🙂 Perfect timing for this recipe. Thanks a Danielle!