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Delicious and moist vegan lemon poppy seed muffins that can be made just vegan OR vegan and gluten-free, instructions for both ways are included. Plus, you can make them extra special by making a lemony glaze for them or you can just enjoy them plain, they’re delicious either way!

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If you've browsed around my website a little, it will be clear, pretty quickly, that muffins are a staple around here! (you can see all of my muffin recipes by clicking here)
I've wanted to share a vegan lemon poppy seed muffin recipe for a while but I had a hard time getting the base of the recipe right.
I always mention that vegan gluten free baking can be tricky if you're new to it. Actually, it can be tricky for anyone! I've been doing it for years, but I still get tripped up at times.
So after another failed attempt with this recipe, I went back to my strawberry muffin recipe and used that as a guide. I made a few changes and happily, it just took a few tests to come up with the recipe I'm finally sharing with you today. So let's get into the details so you can make them, too!
Are you new to vegan gluten-free baking? If so, be sure to read all of my vegan gluten-free baking tips!
Ingredients You'll Need
As with all of my other muffin recipes, the ingredients are minimal and simple. If you keep your pantry stocked well, you likely have all the ingredients to make this recipe, right now!
Flour - You'll need to use all-purpose white flour for this recipe.
Make it gluten-free: Use Bob's Red Mill All-Purpose Gluten-Free Flour Blend in the RED bag for vegan gluten-free lemon poppy seed muffins. Any other gluten-free flour on its own, like almond, oat, or coconut flour, will NOT work, it must be this specific blend to get the same results I do.
NOTE: To ensure your muffins turn out perfectly, it's important to measure the flour accurately (no matter what type you are using!). Check out my step-by-step "How to Measure Flour Correctly" before you start baking.
Sugar – I use organic cane sugar in this recipe. I have not tried making this recipe with liquid sweeteners (like maple syrup or agave) or sugar alternatives, so I am unsure how they would work.
Applesauce - Use unsweetened, unflavoured applesauce. It helps keep the muffins moist and replaces some of the oil, reducing the amount needed.
Oil - Use a neutral-flavoured vegetable oil like refined avocado, safflower, or sunflower. You can also use melted coconut oil. I haven't tried making this recipe without oil.
TIP: If you use coconut oil, make sure the other ingredients are at room temperature to prevent it from solidifying.
Flax Eggs – This recipe is egg-free, using ground flax seeds and water as a vegan egg replacement. You can also use chia eggs instead of flax.
Lemon Juice and Lemon Zest – These are both essential to give the muffins their lemon flavour.
Baking Powder and Baking Soda - Ensure both are fresh, they are important for the muffins to rise and have the proper texture.
Salt and Vanilla - You'll need a little of each to help enhance the flavour.
Poppy Seeds - You can find poppy seeds along with the spices at your grocery store.
How to Make Them
(Note: I’ve outlined the step-by-step on how to make this recipe here, but find the full recipe, ingredients, and directions at the end of this post.)
The first step towards making these delicious vegan lemon poppy seed muffins is to make the flax eggs. Once made, set aside to thicken.
Next, mix the wet ingredients in one bowl and the dry ingredients in another bowl. Then add the wet to the dry ingredients and mix well.
After that, fold in the poppy seeds and you're now ready to scoop the batter into your muffin pan.
I like to use a scoop for dividing the batter, this is the one I have (you can see it in the picture below). It’s actually an ice cream scoop but it doubles perfectly as a muffin scoop.
The vegan gluten-free version of these muffins can over bake in the blink of an eye which causes them to dry out.
I learned this the hard way when testing the recipe when I baked a couple of batches for a few minutes longer than what was needed, so be sure to keep an eye on them as they come close to the end of their baking time.
Once the muffins are done, remove the pan from the oven and carefully transfer each of them to a cooling rack.
You now have 12 of the most delicious lemon poppy seed muffins waiting to be devoured!
Storing Leftovers
Once they've cooled, store them in an airtight container, at room temperature. The version made with all-purpose flour will keep for 4-5 days
The gluten-free version will keep for about 2-3 days. I find that the things I bake with gluten-free flour blends start to stiffen up as if they're stale, the day after being made. They're not stale, it's just the nature of the gluten free flour blend. If this happens, a quick few seconds in the microwave will bring them right back to the same delicious freshness from day one.
Freezing
Once they've fully cooled, wrap them up tightly so they’re airtight, place in a container or freezer bag and freeze. They will keep in the freezer for up to two months.
What's the Texture Like?
These vegan lemon poppyseed muffins are soft, fluffy, light, moist, and perfect. Have a look above to get a visual of what they look like inside.
And when you bite into one, you'll get a burst of bright lemon flavour, thanks to the fresh lemon juice and the lemon zest, and you'll also get little pops of crunch from the poppy seeds.
To Glaze? Or Not to Glaze?
Many lemon poppy seed muffins include a glaze, so I've included steps on how to make vegan lemon drizzle for these muffins, just in case you want to make them a little extra special.
If you do choose to add a glaze, make sure your muffins are almost cooled, a muffin that is still too warm will soak in all of the glaze and it won't remain on top. They'll still taste good, they just may not look the best.
To avoid that, add the glaze when they've almost fully cooled and right before serving, to avoid any mishaps.
(And if the glaze isn't your thing, how about topping them with a little vegan lemon curd?)
If You Make This Recipe...
Please let me know! You can do so by leaving a comment and star rating below or you can also share a pic of your vegan lemon poppy seed muffins with me on Instagram, just be sure to tag me so I can see your pic, I'm @delightfuladventures on IG.
If You Like This Recipe...
You may also like these other simple vegan muffin recipes:
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Fluffy Vegan Lemon Poppy Seed Muffins
Suggested Equipment:
Ingredients:
- 2 tablespoons ground flax seeds
- 6 tablespoons water
- 2 ¼ cups (281g) all-purpose flour **see below for gluten-free directions and important notes about using gf flour**
- 2 teaspoons baking powder
- ¼ teaspoon baking soda
- ¼ teaspoon salt
- ½ cup (120ml) oil (plus extra for greasing muffin tin)
- ½ cup (100g) sugar
- ¾ cup (185g) plain unsweetened applesauce
- 3 tablespoons fresh lemon juice
- 1 teaspoon lemon zest
- 1 teaspoon vanilla extract
- 2 tablespoons poppy seeds
Lemon Glaze (Optional)
- ½ cup (60g) powdered sugar
- 1 tablespoon lemon juice
- ¼ teaspoon lemon zest
Instructions:
- Preheat oven to 350° F (177° C).
- Prepare your flax eggs by whisking together ground flax seeds and water. Set aside to thicken.
- Line a muffin pan with liners or generously grease the inside of each cup with oil.
- In a small bowl, whisk together the flour, baking powder, baking soda, and salt. Set aside.
- In a medium bowl, mix the oil, sugar, applesauce, lemon juice, lemon zest, vanilla, and flax eggs together until blended.
- Slowly add the dry mixture to the wet mixture and stir until combined. Fold in the poppy seeds.
- Using a spoon or a large scoop, divide batter into the 12 muffin cups.
- Bake for 18-20 minutes or until toothpick inserted in the middle of the largest muffin comes out clean. If you are making the vegan gluten-free version, bake for 15 minutes.
- Let muffins cool in muffin pan for a few minutes and then remove and place them on a cooling rack.
To Make Lemon Glaze (Optional):
- Add the powdered sugar to a small bowl and a little at a time, add the lemon juice and whisk until you have a smooth glaze. You may not need the full tablespoon of lemon juice, depending on how thick you want it. If you add all the juice and it's too thick, add a little more juice, if it's too thin, add a little more powdered sugar. Add the lemon zest and mix until it has been incorporated into the glaze.
- Drizzle onto muffins just before serving.
Video:
Recipe Notes:
- Please read all of the information above and below before making this recipe.
- If using gluten-free flour, use (2 ¼ cups / 315g) and bake the muffins for 15 minutes or until a toothpick comes out clean from the largest muffin).
- It's important to know that different gluten-free flour blends use different ingredients and ratios, so results will always vary if you substitute. I have never used any other brand of flour to make this recipe (other than Bob's Red Mill Gluten Free All Purpose Baking Flour (Amazon link) with the red label, NOT the blue label), so please know that your results may not be the same as mine if you substitute with another gluten-free flour blend. The weight listed above is for this specific brand of flour.
- This recipe will NOT work with coconut flour or any other single gluten-free flour like oat or almond, it must be the blend mentioned above fo the intended results.
- Store leftovers in an airtight container. See above for more storage info.
- The nutrition info listed below is based on one muffin with the recipe made as written. The muffins made with gluten-free flour have a calorie count of 207 per muffin. Nutrition info is only to be used as a rough guide. Click here to learn how nutrition info is calculated on this website.
Bernadette says
Hi Gwen, THANK YOU so much for this recipe...I've been baking for many years as my family has celiac and can't have dairy nor eggs. I've searched alot for a nice recipe for lemon poppy muffins and yours is just AMAZING!!! I love the way you explain how to measure and which flours to use and not. My family judged these the BEST, bakery style muffins. However I only substituted with coconut yogurt instead of the applesauce and followed all your instructions, as you mentioned, it was ok to do so and they were so very moist. Making another batch tomorrow lol
Gwen Leron says
You're welcome, Bernadette! It makes me so happy to know that you and your family like the recipe so much. I hope your second batch came out just as perfect as the first. Enjoy!
Janelle says
Can you make these with spelt flour? I have light spelt and whole grain spelt flour. Thanks!
Gwen Leron says
Hi Janelle, I have not tested the recipe with spelt flour so I'm really not sure how they would turn out. According to this article: https://www.bonappetit.com/story/spelt-flour you can use the light spelt flour as a 1 to 1 sub for the all-purpose flour. If you decide to experiment, please come back and let me know how it turned out!
Cassie says
Made these yesterday and they turned out very chewy and thick… I used a gluten free blend that I made because I can’t have almond flour or potato starch. I used a vegan egg replacement. I’m also in Boulder at 5300 ft above sea level. I’m new at vegan and gluten free baking so I am wondering what I can do to make them fluffy. 🙂
Gwen Leron says
Hi Cassie! I'm sorry they did not turn out properly for you. I think the issue may be with the flour you used, it could also be with the egg replacement since some of them can make recipes turn out gummy. All gluten-free flour blends, whether homemade or store-bought, work differently, they are not all 1-to-1 substitutes for one another. The flour blend I use does contain potato starch so what I would suggest is to look for (or make) a blend that is uses the same group of ingredients in the blend I use but use a different starch other than potato. Then you would have to experiment a little bit. I don't have any experience with high altitude baking, but this article may help you: https://www.kingarthurbaking.com/learn/resources/high-altitude-baking I hope all of this helps!
Shannon says
Can I use coconut sugar instead?
Gwen Leron says
Hi Shannon. Yes, you can, the only thing that will be different is the colour of the muffins, they will be darker. Let me know how things go!
Leah says
I just made these and I can't have coconut so I used olive oil and they cooked on the outside but the inside is all batter and I've cooked it for 15 more mins and it still didn't come out, I also used chia seeds instead of flax what do you think I did wrong
Gwen Leron says
Hi Leah, they definitely should not turn out like that. Did you make and changes to the way the recipe is written? Did you change any ingredients other than the oil and chia? And the most important question, what kind of flour did you use? If you were making the gluten-free version, did you use the same brand I mention to use? All gluten-free flours perform differently, they are not all interchangeable so a change to the flour can cause this. Let me know and I'm happy to help troubleshoot further!
Mary says
Hi!
Can I make these without the poppyseeds …. I am looking for a good Vegan GF cake to use as a lemon cupcake and I love all your recipes… wondering if omitting the poppyseeds would cause a problem?
Thanks!
Gwen Leron says
Hi Mary! Leaving out the poppyseeds will not cause any problems at all, so it will be fine! Enjoy 🙂