Healthy Lemon Poppy Seed Muffins
Breakfast,  Desserts,  Snacks

Healthy Lemon Poppy Seed Muffins (Gluten-Free + Easy!)

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You only need one bowl to make these easy, healthy lemon poppy seed muffins! They’re completely gluten-free, refined sugar-free, and have an easy dairy-free option. The perfect combo of moist and fluffy!

lemon poppy seed muffins gluten free

Lemon Poppy Seed Muffins With Yogurt

If you’ve been around the Shh Kitchen for a while, you know that I LOVE adding yogurt into so many of my recipes. Such as my, Chocolate Chip Cookie Brownie Skillet, Chocolate Peanut Butter Protein Overnight Oats, THE BEST Healthy Cheesecake, and so many more

I specifically use plain nonfat greek yogurt to boost the protein and cut down on unnecessary fats in my recipes. Plain nonfat greek yogurt also adds healthy probiotics as well! Interested in learning more about greek yogurt? Here’s an amazing article talking all about the benefits of greek yogurt. You can use a dairy-free yogurt to keep these lemon poppy seed muffins dairy-free!

healthy lemon muffins

Low Sugar Lemon Muffins

What’s not to love about a low sugar muffin? Not only are these healthy lemon muffins low in sugar, they’re actually made with all UNREFINED sugar! Staying away from refined sugars is so important when wanting to maintain a healthy diet. We use honey to sweeten these gluten-free lemon muffins, but you can also use 100% pure maple syrup.

Some of my favorite recipes from the Shh Kitchen are made with honey! My Healthy Pumpkin Muffins, Easy Peanut Butter Granola, or my Lemon Blueberry Banana Bread are just a few favorites. 

easy lemon poppy seed muffins

How To Make Healthy Lemon Poppy Seed Muffins

You only need one bowl to whip up these healthy lemon poppy seed muffins!

  1. Mix all your wet ingredients together until smooth.
  2. Fold in your dry ingredients.
  3. Scoop into muffin tin.
  4. Bake at 350 F. for 12-15 minutes.
  5. Let cool for 10 minutes, then drizzle with lemon cream cheese glaze and devour!

Healthy Gluten-Free Lemon Muffins

What makes these lemon muffins gluten-free you ask? Well, we use a combination of oat flour and a little almond flour. Oat flour is one of my absolute favorite healthy flour alternatives. It’s rich in fiber and loaded with vitamins and minerals. You can read more about the benefits of oat flour and find other healthy flour alternatives here! 

Oh, and if you’re wondering where you can buy oat flour, don’t even consider it. MAKE IT YOURSELF in your food processor or high speed blender. Just follow my step by step blog post on how to make oat flour!

oat flour lemon muffins

The Best Gluten-Free Lemon Poppyseed Muffins

These muffins are hands down the BEST! Here are a few reasons why:

  • So fluffy!
  • Perfectly Moist (without using a ton of oil!)
  • Done in 20 minutes or less!
  • Amazing with the healthy lemon cream cheese glaze!

I cannot wait for you to give this healthy lemon poppy seed muffin recipe a try! Please snap a picture and share it with me! Seeing your kitchen creations makes my day and encourages me to keep creating new recipes for you!

the best lemon poppy seed muffins

Happy Muffin Makin’!

More Healthy Lemon Recipes


healthy lemon poppy seed muffins pinterest
Yield: 12 Muffins

Healthy Lemon Poppy Seed Muffins (Gluten-Free)

Healthy Lemon Poppy Seed Muffins

You only need one bowl to make these easy healthy lemon poppy seed muffins! They’re completely gluten-free, refined sugar-free, and have an easy dairy-free option. The perfect combo of moist and fluffy!

Prep Time 8 minutes
Cook Time 12 minutes
Total Time 20 minutes



  • 1 Egg
  • 1 tsp Almond Extract (can omit or sub vanilla extract)
  • ⅓ Cup Honey or Pure Maple Syrup
  • 2 Small Lemons (you will need the zest of 2 and the juice of 1½) (About 1 Tbs zest + 3 Tbs juice)
  • ¼ Cup Plain Yogurt (I used nonfat greek. Or sub dairy-free yogurt)
  • 2 Tbs Melted Coconut Oil
  • ¼ Cup Water


  • 1½ Cups Oat Flour (make your own with any kind of oats)
  • ½ Cup Blanched Almond Flour (I use this brand)
  • ⅛ tsp Pink Himalayan Salt
  • 1½ Tbs Poppy Seeds
  • 2 tsp Baking Powder

Optional Lemon Cream Cheese Glaze

  • 3 Tbs Softened Low Fat Cream Cheese (Can Sub Vegan Cream Cheese or Regular Cream Cheese)
  • 3 tsp Pure Maple Syrup or Honey (or to taste)
  • ¾ - 1tsp Plant Based Milk (or Milk of Choice or Water)
  • 1½ tsp Fresh Lemon Juice
  • ½ tsp Fresh Lemon Zest
  • Opt: ⅓ tsp Vanilla Extract


1. Preheat oven to 350 F. and line a muffin tin with silicone muffin liners, paper liners, or grease with coconut oil.

2. In a medium bowl, combine all the wet ingredients and whisk until smooth.

3. To the wet mixture, fold in the oat flour, almond flour, salt and poppy seeds. Then fold in the baking powder until just combined.

5. Divide the batter evenly among muffin tins, filling each almost to the top (should fill 12 muffin cups).

6. Bake at 350 F. for 12-15 minutes until a toothpick comes out clean or with just a few moist crumbs. Optional: While the muffins bake, make lemon cream cheese icing by combining softened cream cheese, maple syrup, plant based milk, lemon juice and lemon zest in a medium bowl. Beat with an electric hand mixer or fork until smooth. Add more or less liquid to get desired glaze consistency.

7. Let muffins cool for 5 minutes before transferring out of pan. Top with homemade lemon cream cheese icing and enjoy!

8. Store in an airtight container on the counter for up to 4 days, in the fridge for a week or freezer for up to 3 months.


  1. Egg Substitute: I have not tested a flax egg, but if you do, use 1 Tbs ground flax + 2 Tbs water. Let me know how they turn out if you try!
  2. Don’t have almond flour? I have not tested this recipe with just oat flour, but if you try this, perhaps add a touch more honey. Let me know if you make them this way!
  3. Lemon Cream Cheese Glaze: add more or less liquid to get desired consistency.

Use code "shh20" for FREE SHIPPING off your online nut-butter orders at Georgia Grinders

Be sure to tag @secretlyhealthyhome on Instagram, Facebook or Pinterest with a picture of your recipe! I love seeing your kitchen creations so please leave a comment and rate the recipe if you make it! It really helps support me!

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Nutrition Information:



Serving Size:

1 muffin without glaze

Amount Per Serving: Calories: 143Total Fat: 6gCarbohydrates: 18.3gNet Carbohydrates: 17.2gFiber: 1.1gSugar: 5.8gProtein: 4g

Did you make this recipe?

Be sure to tag @secretlyhealthyhome on Instagram, Facebook or Pinterest with a picture of your recipe creation! Please leave a star rating and or comment! It really helps support me and encourages me to keep making recipes for you!

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  • Lauren

    So good! I didn’t add any almond flour instead I did 1/4 cup of protein powder. Thank you for delicious healthy recipes!!

    • Claire

      Hi Lauren! I am so glad you enjoyed these muffins! Yay! Also, love how you made them nut-free by using protein powder! Brillant!!! 🙂

  • Shauna

    Excellent recipe! Mine turned out well.

    • Claire

      Yay! I’m so happy to hear that! Thank you for sharing your success! 🙂

  • Angela

    Hi Claire!! I love all your recipes!! Super healthy and delicious!!! Thank you for sharing! ❤🙏🥰

    • Claire

      Hi Angela! Awh I am so glad you love my recipes. Makes my day to hear that!
      Happy Healthy Baking!


  • Larissa

    Sad mine didn’t raise. I followed the recipe exactly.

    • Claire

      Hi Larissa! So sorry yours didn’t rise. Did you check the expiration date of your baking powder? Also, depending on where you live this could affect the rise. Are you somewhere with high elevation?

      • Rachael

        Hi – can you use wheat flour instead (I know this stops it being gluten free!)? Thank you

        • Claire

          Hi Rachael! Yes, you most definitely can substitute the oat flour for wheat flour. I haven’t tested this, but it should turn out well. Let me know if you try it 🙂

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