These healthy lemon poppy seed muffins are loaded with the classic and bright lemon and almond flavor, but without any sugar or highly processed flour! They have a soft, well-formed texture and make a yummy, satisfying breakfast treat.

These Healthy Lemon Poppy Seed Muffins Are:
- Naturally sweetened
- Free of highly processed flours
- Easily made gluten free
- Vegan
- Healthy
- Hearty & filling
- Low glycemic
- Perfect on-the-go
- Freezer friendly
- Delicious!
Common Questions About This Recipe
Can I make these without any sweetener?
- Yes, but these really do benefit from just a touch of sweetness as there is nothing else to sweeten them. If you’re looking for a completely sweetener-free way to enjoy these lovely spring flavors, I recommend adding almond extract, lemon zest, and poppy seeds to these breakfast cookies. The naturally sweetness from the mashed banana in that context works beautifully.
Can I just use oats instead of flour?
- If you prefer not to eat flour and it makes you more comfortable, you could pulse some oats and almonds in a food processor to a consistency that works for you. The more finely they are ground, the better the texture of these muffins will be.
Substitutions & Modifications
- I always make these lemon poppy seed muffins vegan, but if you want to swap in dairy milk for the non-dairy milk in the recipe, it should work great.
- You can swap the almond butter for coconut oil in this recipe, both work great. A little bit of oil or fat is important though!
- Feel free to swap the honey for your sweetener of choice.
- This recipe uses a flax “egg” for binding. If you prefer, you could swap the flax seeds for 1 tbsp of chia seeds, or you can reduce the water to 1/4 cup and use a real egg.
- If you’re making these for dessert or serving these to people without any dietary restrictions, you can add a sweet lemon icing drizzle by mixing 1/4 cup of powdered sugar with 2 tsp of fresh lemon juice.
- To make these muffins gluten free, be sure to use certified gluten free oats.
- Feel free to replace the oat flour and almond flour for 3/4 cup of your all-purpose flour of choice. I chose oat flour because it’s easy to make my own in a food processor from rolled oats, and almond flour for the flavor that it lends to these baked goods.

Tips for Success
- Be sure to use fresh squeezed lemon juice and real lemon zest for the best flavor.
- Use paper muffin liners or well-greased muffin tins to prevent sticking. I love my reusable silicone baking cups
- The batter for these treats is too thin and wet to make cookies out of. It won’t hold its shape if poured onto a baking sheet. If it’s cookies you’re after, check out my awesome breakfast cookie recipe.
- I find that a muffin shape works best for this recipe, but if you wanted to make bread I would recommend mini loaf pans rather than regular loaf pans to avoid gooey centers. You’ll need to cook them longer too, but it will depend a bit on your oven and the size of your pans.
More Healthy Baking Inspiration:
- Sugar & Flour Free Baking Hacks
- Banana Walnut Oat Muffins (Sugar & Flour Free)
- How to Make Healthy Breakfast Cookies
- Blueberry & Almond Flourless Oatmeal Muffins
- Strawberry Rhubarb Oatmeal Bars
- Carrot Cake Oatmeal Bars
- Flourless Oat & Seed Rolls
- How to Make Cornbread Without Flour
- Flourless Sweet Potato Brownies
If you make these healthy lemon poppy seed muffins, leave a star rating or comment below! Your feedback is so helpful to me and other readers. You can also tag me in your meal pics on Instagram @katiesconsciouskitchen, or join my free private facebook group to share your creations and inspire others! I love to see what you all are making.

Healthy Lemon Poppy Seed Muffins
Ingredients
Dry Ingredients
- 1 cup instant oats
- 1/2 cup oat flour, see notes to make your own
- 1/4 cup almond flour, see notes to make your own
- 1/2 tsp baking soda
- 1/4 tsp baking powder
- 1 tbsp poppyseeds
- 1/8 tsp salt
- sliced almonds, to garnish
Wet Ingredients
- 1 tbsp ground flaxseed, + 1/2 cup water
- 1/2 cup plant milk, I use soymilk
- 2 tbsp lemon juice
- zest of one lemon
- 1/2 tsp almond extract
- 1/4 tsp vanilla
- 1 tbsp almond butter, or coconut oil
- 1 tbsp honey
Useful Equipment
Instructions
- Preheat the oven to 350°F
- In a small mixing bowl, combine the ground flaxseed into the 1/2 cup of water and let sit for a few minutes to activate their binding properties.
- Stir together the dry ingredients in a mixing bowl.
- Stir all the wet ingredients into the flax “egg” mixture and stir well to combine.
- The batter should be fairly wet. Gently press a few sliced almonds onto the top of each muffin for decoration.
- Fill your muffin tins all the way to the top with batter. Bake for 25-30 minutes, or until they are golden on top and holding together well.
- Allow to cool for at least 15 minutes before enjoying warm or cold.
It says 3 servings. Does that mean this makes 3 muffins?
Hi Lynn, no it makes about 7-9 muffins, depending on how full you fill the tins. I find that 2-3 make a good, filling breakfast, so the whole recipe makes about 3 breakfasts.
Very nice, I made 6 of them, perfect taste for me and I followed the recipe like it is written. Thanks a lot I’m a fan of your way of eating
I’m so glad you enjoyed them! Thanks for the feedback.
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