Lemon Poppyseed Muffins (Gluten-Free)

Heather Dessinger

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Moist and cakey, these lemon poppyseed muffins are like sweet little bursts of sunshine on a stay-in-your-pajamas rainy day . . . or a pop-out-of-bed and hit the road early day . . . or any day, really. Like my five-minute ketchup, super simple cauliflower crust, and homemade chicken nuggets, they’re easy enough to whip up while simultaneously discussing how many eyelids camels have (three) and whether or not all birds can fly (nope).

And of course, we’re using only real ingredients – not the partially hydrogenated oil, modified food starch, yellow number 5, and other stuff you’ll find on store shelves. I hope you love this recipe as much as we do!


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4.63 from 8 votes

Gluten-Free Lemon Poppyseed Muffin Recipe

Make lemon poppyseed muffins with almond flour, honey, and lemon extract and peel for a delicious, easy breakfast.
Course Breakfast
Cuisine American
Keyword gluten-free, muffins
Prep Time 10 minutes
Cook Time 20 minutes
Cool 10 minutes
Total Time 30 minutes
Servings 9 muffins
Calories 264kcal
Author Heather Dessinger


  • muffin pan
  • medium bowl
  • whisk
  • mixing bowl



  • Preheat oven to 350°F. 
  • Grease nine muffin cups or line with cupcake wrappers and set aside.
  • In a medium bowl, stir together all but 2 teaspoons of almond flour, coconut flour, salt, poppy seeds, and baking soda.
  • In a separate bowl, whisk together the eggs, honey, vanilla, lemon extract, and lemon zest. 
  • Add the flour to the egg mixture and mix to combine.
  • Divide the batter evenly between the prepared muffin cups.
  • Combine the cane sugar with the remaining almond flour and sprinkle over the top of the muffins.
  • Bake for about 20 minutes in the preheated oven. The tops should be springy yet firm when they're ready. 
  • Allow to cool for about 10 minutes before removing from the muffin pan.


The sprinkle of natural cane sugar on the top helps keep the muffin moist and also gives a nice crunch of sugar.


Serving: 1muffin | Calories: 264kcal | Carbohydrates: 24g | Protein: 9g | Fat: 16g | Saturated Fat: 2g | Cholesterol: 117mg | Sodium: 283mg | Potassium: 78mg | Fiber: 3g | Sugar: 17g | Vitamin A: 170IU | Vitamin C: 6.4mg | Calcium: 92mg | Iron: 1.8mg

More Yummy Gluten-Free Muffin Recipes

Blueberry Muffins – Moist and cakey, these grain-free muffins are delicious served warm and slathered in butter.

Strawberry Streusel Muffins – These muffins pair a rich, cakey batter with a crunchy, crumbly streusel topping, and they’re surprisingly easy to make.

Banana Walnut Muffins – These muffins only take about 5 minutes of hands-on prep, and they make a yummy breakfast or afternoon snack.

Chocolate Zucchini Muffins from Danielle of Against All Grain – Infused with cacao powder, cinnamon, nutmeg and chocolate chips, these zucchini muffins are perfectly moist and totally delicious.

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Heather is a holistic health educator, herbalist, DIYer, Lyme and mold warrior. Since founding Mommypotamus.com in 2009, Heather has been taking complicated health research and making it easy to understand. She shares tested natural recipes and herbal remedies with millions of naturally minded mamas around the world. 

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39 thoughts on “Lemon Poppyseed Muffins (Gluten-Free)”

    • The sucanat is not necessary, although it adds a little extra sweetness. Lemon extract has a much stronger flavor than lemon juice, so the flavor would be very faint with just the juice. 🙂

      • Heather what is sucanat? I am really in joying your recipes and also things that you post about your family and friend you are truly a down to Earth person.Thanks again..??

    • Hi Heather, thank you for the “tried and true” recipe. I have a question about honey – I’ve seen it in many sources that heated up to 60 Celsuis it becomes toxic. What do you think of that? Thank you!

    • I use lemon zest from organic lemons and I think it’s far superior to lemon extract! And I am famous for my lemon recipes, have even won prizes. Can’t wait to try this with zest!

  1. Hi Heather,
    I am wondering why you cook honey in the oven in this recipe and yet your very careful to not add honey to a warm concoction because of not wanting to destroy any of the neutriants in the honey in your ginger juice video. I think about this often and hope you can clarify it for me. Thanks, Gloria

    • Hi Gloria, in many cultures honey is considered medicinal, both topically and as a food. When I’m baking with it for enjoyment I don’t mind heating it, but when I’m preparing it as part of a remedy I prefer not to heat it so that its enzymes are preserved.

      • Thank you so much for responding. Digging a little deeper ~ somewhere, awhile ago, I think I read that it can be harmful to heat ‘raw’ honey, I think behind loosing the enzymes. That’s why I was wondering. Planning on baking up the muffins soon. I probably will do my usual substitute – a tad of maple syrup, with the balance of Stevia or Just Like Sugar to taste. Gloria

        • I have heard the same thing about honey but have never found any research or solid information that supports it. I think these would be great with maple syrup, but I’m also personally comfortable using honey (especially since it’s a more affordable option where I live.)

  2. Hi Heather,
    I went to the store today to grab all the ingredients and there was vanilla extract and vanilla flavoring on the shelves. The extract contains alcohol and the flavoring contacts glycerin. Just wondering which I should use? They are both organic. Along the same lines, I had to grab lemon flavor as I did not see lemon extract. Hope that is ok?

    Also, they were out of Baking Soda but I do have Baking Powder, which contains Sodium Bicarbonate (plus Cornstarch and Monocalcium Phosphate). Can I use the Baking Powder instead?

    • Without knowing the exact brands I’m only guessing, but “flavoring” typically means that it tastes like vanilla but is actually something else, while extract implies that it is actual vanilla extracted in alcohol. Vanilla can be extracted in glycerin as well, so it’s possible that both are extracts. It’s hard to say without seeing the label. Baking powder is basically baking soda with an acid (cream of tartar) added to activate it. In some baked good with no acid that’s necessary. These muffins do have an acid in them so the additional acid is not needed, but it won’t hurt them. You will need to use more though since only a portion of the baking powder is actually baking soda. I’m not sure by how much – perhaps there is an online calculator that can help.

      • Thank you, Heather! The Vanilla Flavoring is by Frontier Co-op. The bottle states that it is Organic, Non-Alcoholic and made from Vanilla Oleoresin. Specifically the ingredients are Organic Glycerin and Organic Vanilla Bean Extractives in Water. The Vanilla Extract is the Organic Whole Foods brand and the ingredients are Organic Water, Alcohol and Vanilla Bean Extractives. So it appears they are both extracts, but one with alcohol and the other with glycerin. Is one particularly more “safe” or healthier than the other? I am extremely new to baking, so apologies for all the questions!

        • Both are totally fine. I’ve made extracts with both alcohol and glycerin, and they both work beautifully in baked goods.

  3. 5 stars
    I have finally found a natural recipe guru! Heather, these are amazing! These don’t taste like a substitute for a typical muffin, they are just as good as the traditional thing. Both of my kids loved them and my husband, which is really saying something. He’s highly critical of all my healthy baked goods, and he loved these. I actually didn’t even have a lemon so I just used lemon extract and they still tasted great!