Healthy Lemon Poppy Seed Muffins

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:

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

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.
5 from 4 votes
Print Pin Ratings & Comments
Active Time: 15 minutes
Inactive Time: 25 minutes
Cooling Time: 15 minutes
Servings 3


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


  • 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.


How to Make Oat or Almond Flour:To make your own oat or almond flour, place sliced almonds or oats in a blender or food processor and pulse until as finely ground as you prefer. The more finely ground they are, the more absorbent it will be and the better the texture of your baked goods. I like to process them separately so I can measure them separately, and because they each take different amounts of time to process.
Substitutions: Instead of flax seed you can use chia seeds. Or, if you want to substitute a real egg instead of a “flax egg,” reduce the amount water to 1/4 cup and omit the flax seeds.
Storage: Store in an airtight container in the fridge for up to 4 days, or freeze for up to a month.
Optional Lemon Icing Drizzle: Mix together 1/4 cup powdered sugar and 2 tsp fresh squeezed lemon juice for an optional sweet drizzle.

Nutrition Information

Calories: 355kcal (18%)Carbohydrates: 46g (15%)Protein: 12g (24%)Fat: 15g (23%)Saturated Fat: 2g (13%)Trans Fat: 1gCholesterol: 4mg (1%)Sodium: 342mg (15%)Potassium: 319mg (9%)Fiber: 8g (33%)Sugar: 9g (10%)Vitamin A: 69IU (1%)Vitamin C: 4mg (5%)Calcium: 199mg (20%)Iron: 3mg (17%)
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  1. Lynn Holloway

    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.

  2. fabienne

    5 stars
    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

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