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Home » Recipes » Snacks

Lemon Poppyseed Oat Flour Muffins

Last Modified: May 26, 2025 · Published: Jan 23, 2024 by Janessa · 4 Comments
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These lemon poppyseed muffins are made entirely with oat flour for a gluten free twist. Packed with fresh lemon flavor and topped with crunchy sugar, you'll love their moist and fluffy crumb.

Jump to:
  • The Ingredients
  • The Method
  • Leftovers and Storage
  • Make it Your Own
  • Serving Ideas
  • More Oat Flour Recipes...
  • Recipe Card
  • Comments
Lemon poppyseed muffin with a bite taken out.

Made entirely of whole grain oats, I have come to love using oat flour for many reasons.

In fact, from cookies to banana bread, it is my go-to flour for the majority of my baking.

After carefully honing my oat flour cookie skills, I got curious about oat flour-based muffins.

Stack of lemon poppyseed muffins.

Because of the lack of gluten in oat flour, it can be a bit more finnicky to bake with than wheat flour. You can easily end up with muffins that either crumble right apart or are incredibly dense and gummy.

Neither of which I wanted.

I experimented with with applesauce, banana, blueberry and pumpkin muffins among others, and eventually landed on the ideal ratio of ingredients and best process for the right texture and delicious taste.

Today's version are like sunshine in a muffin with a bright burst of lemon flavor in each bite. (These Lemon Recipes all taste like a bite of sunshine.)

If you're new to baking with oat flour, I've got plenty of tips to ensure your lemon poppy seed muffins turn out just right.

So let's get baking!

The Ingredients

Ingredients for oat flour lemon poppyseed muffins.
  • Oat Flour- If you need the recipe to be gluten free, ensure you use certified gluten free oats/oat flour.
    • I recommend sifting the oat flour first if it is lumpy so that you don't have to overmix the muffins.
    • For best results, use store-bought oat flour.
    • To Measure Oat Flour: If you have a kitchen scale, that is best for most accurate measurements of oat flour. But if you are measuring by hand, I have found that I can consistently achieve 120 g per cup of oat flour by scooping the oat flour into a measuring cup, lightly packing it down and then levelling off the top. See this oat flour snickerdoodles post for more details.
  • Baking Soda and Baking Powder- Oat flour isn't the same structurally as regular flour so it needs a little extra help to achieve the same lift.
  • Fine Sea Salt- Regular salt can be used as well.
  • Poppy Seeds- If you just want a lemon muffin, feel free to leave them out. Or substitute with chia seeds.
  • Pure Maple Syrup- Honey or agave will also work but not a granulated sweetener. For more info, check out this post on Maple Syrup Substitutes. As written, these muffins aren't overly sweet- if you prefer, you can add an additional tablespoon.
  • Avocado Oil- Melted coconut oil, canola oil or olive oil can be used instead. If using melted coconut oil, it is imperative that all of the ingredients be at room temperature so that it doesn't harden in the batter.
  • Greek Yogurt- This is a key for structure and moisture. For an alternative, you can use sour cream, coconut yogurt for dairy free or check out this post on Greek yogurt substitutes.
  • Lemon- You will need both the juice and the zest from one large lemon in order to infuse the muffins with enough citrus flavor. If you want to up the lemon flavor even more, you can add ½ teaspoon of pure lemon extract.
  • Egg
  • Coarse Sugar- (Optional- but not really..) Sprinkle on before baking for a crunchy topping.

The Method

1. Mix dry ingredients. In a large mixing bowl, whisk together the oat flour, poppyseeds, baking soda, powder and salt.

Dry ingredients in a mixing bowl.

2. Mix wet ingredients. In a medium bowl, combine the maple syrup, oil, Greek yogurt, eggs, lemon juice and lemon zest.

Wet ingredients in a mixing bowl.

3. Combine. Pour the wet mixture into the dry and stir until just combined.

Wet and dry ingredients combined in a large mixing bowl.

4. Divide into muffin tins. Line a regular muffin tin with 8 silicone muffin cups or paper liners. Fill the muffin liners nearly to the top with the muffin batter.

Muffin batter divided into a muffin tin.

Sprinkle about ¼ teaspoon of coarse sugar over each.

Coarse sugar sprinkled over top of muffins prior to baking.

5 . Bake. Bake at 375 F for 20-25 minutes until a toothpick inserted comes out mostly clean and the muffin bounces back slightly when you press on the center.

Oat flour lemon poppyseed muffins in a tin after baking.

6. Cool and enjoy. Allow these moist gluten-free lemon poppyseed muffins to cool in the muffin pan for 5 minutes and then move to a wire rack to cool completely.

Leftovers and Storage

To Store: Cool oat flour lemon poppyseed muffins completely and then store in an airtight container at room temperature for up to 3 days.

To Freeze: Cooled muffins can be frozen for up to 3 months.

Muffins on a countertop.

Make it Your Own

Mini Muffins: Line a mini muffin tin for enough for 24-30 muffins and fill liners nearly full. Bake for 10-12 minutes.

Add a Glaze: Once cooled, mix together 1 tablespoon of lemon juice with ¼ cup of powdered sugar and drizzle over the top.

Use a Different Citrus: You can try swapping out the lemon juice and zest for lime, orange or even grapefruit. Omit the poppyseeds if you would prefer.

Hand holding an oat flour lemon poppyseed with a bite taken out.

Serving Ideas

Enjoy these lemon poppyseed muffins make for a delicious snack or easy breakfast for busy mornings (maybe alongside some Egg White Bites Recipe or an Avocado Spinach Smoothie).

Can I Use Homemade Oat Flour?

For best results, I strongly recommend using store-bought oat flour as the consistency of homemade oat flour can be variable.

More Oat Flour Recipes...

  • Spoon dipping into a mug of oat cake.
    Oat Mug Cake
  • Stack of chocolate chip cookies made with oat flour.
    Oat Flour Chocolate Chip Cookies
  • Piece of oat flour bread being buttered.
    Oat Flour Bread
  • Strawberry crisp with oatmeal topping in a bowl.
    Strawberry Oatmeal Crisp

Recipe Card

Fluffy lemon poppyseed muffin with a bite taken out.

Oat Flour Lemon Poppyseed Muffins

Made entirely with oat flour, these lemon poppyseed muffins are naturally sweetened and gluten free, with fresh flavor and a fluffy crumb.
5 from 32 votes
Print Pin Rate
Prep Time: 20 minutes minutes
Cook Time: 20 minutes minutes
Total Time: 40 minutes minutes
Servings: 8
Calories: 178kcal

Ingredients

  • 1 and ¼ cup oat flour certified Gluten Free, if needed
  • 1 tablespoon poppyseeds
  • ½ teaspoon baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt
  • ⅓ cup Greek yogurt
  • ⅓ cup lemon juice about 1 large
  • ¼ cup avocado oil or canola oil
  • 3 tablespoon pure maple syrup or melted honey
  • 2 teaspoon lemon zest from about 1 large
  • 1 egg
  • 2 teaspoon coarse sugar optional
US Customary - Metric
(Prevent your screen from going dark)

Instructions

  • Preheat the oven to 375 °F. Line a muffin tins with enough for 8 muffins.
  • In a large bowl, whisk together oat flour, poppyseeds, baking soda, baking powder and salt.
  • In a medium bowl, combine maple syrup, oil, Greek yogurt, egg, lemon juice and zest.
  • Pour the wet ingredients into the dry and mix until just combined.
  • Fill the prepared muffin tin liners ¾ full and sprinkle ¼ teaspoon of coarse sugar on each. Bake for 20-25 minutes until a toothpick poked in the center comes out mostly clean or the centers bounce back when lightly pressed.
  • Allow to cool in tins for 5 minutes and then remove to a wire rack to allow to cool completely.

Notes

Leftovers
Cool leftover muffins completely and store in an airtight container in the refrigerator for up to 3 days or freeze for up to 3 months.
Mini Muffins
Line a mini muffin tin for 24-30 muffins and fill liners nearly full. Bake for 10-12 minutes.

Nutrition

Calories: 178kcal | Carbohydrates: 19g | Protein: 5g | Fat: 10g | Saturated Fat: 1g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 6g | Trans Fat: 0.003g | Cholesterol: 21mg | Sodium: 183mg | Potassium: 125mg | Fiber: 2g | Sugar: 5g | Vitamin A: 31IU | Vitamin C: 5mg | Calcium: 63mg | Iron: 1mg
Did you make this recipe?Let me know what you thought in the comments below!

Want to learn more about oat flour? Check out these resources!

  • The Ultimate Guide to Oat Flour
  • Oat Flour vs. Wheat Flour
  • The Best Oat Flour Recipes
  • Oat Flour Cookie Tips
  • Oat Flour Muffin Tips
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  • Baked oats in a ramekin topped with berries and nut butter.
    Microwave Baked Oats
  • Stack of copycat eat-more bars.
    Eatmore Bars (Healthy Copycat)
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Comments

    5 from 32 votes (31 ratings without comment)

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  1. Meaghan says

    April 01, 2025 at 8:30 pm

    5 stars
    really delicious! for me it only made 4 muffins but i filled them up so the top would get crusty, and it did!! surprisingly they don’t taste much like oats which is nice. i made these lime poppy added a lime glaze and it was a reallyyy nice touch.

    Reply
    • Janessa says

      April 02, 2025 at 11:12 am

      I'm so glad you liked these muffins, Meaghan! Thank you for taking the time to leave this kind review!

      Reply
  2. Angela says

    August 07, 2025 at 12:57 am

    Could you add fresh blueberries to this recipe?

    Reply
    • Janessa says

      August 07, 2025 at 6:08 am

      Hi Angela, I haven't tried it but suspect it would be great! Let me know if you give it a try.

      Reply
Janessa

Hi, I'm Janessa and I'm passionate about sharing recipes that are made with wholesome ingredients, are quick and easy and most importantly, delicious!

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