Keto Lemon Poppyseed Muffins

Annie Lampella @ Ketofocus

By Annie Lampella, Pharm.D.

Published April 8, 2024

Reader Rating
5 Stars (1 Reviews)

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Tangy keto lemon poppyseed muffins are ultra moist inside and take about 25 minutes to make from start to finish!

Costco poppyseed muffins were my absolute favorite in high school. It was obvious my thighs also loved them because that’s where they went… straight to my thighs. LOL! Since I’ve been making low-carb muffins like keto gingerbread muffins and chocolate zucchini muffins, I found a way to still enjoy this fluffy grab-and-go baked good without the worry of packing on the lbs! Plus, I added lemon to these!!

Baked muffins filled with poppyseeds in a muffin tray.

What makes these muffins keto?

  • Uses keto flours – Instead of wheat based flour, this recipe uses almond flour and coconut flour. I like the combination of the two flours. When used together they provide a similar consistency to all-purpose flour.
  • Sugar-sweetener – Instead of sugar, I use sugar-free sweeteners. Look for a sweetener with a combination of either monkfruit, erythritol, stevia or allulose. Combination sweeteners taste and act more like baking sugar. Plus many measure cup for cup with sugar.
  • Still fluffy thanks to key ingredient – One of the downsides of not using all-purpose flour is that most keto flours don’t contain gluten. Gluten is what helps to create fluffy muffins with a puffy muffin top. To get the same results, this muffin recipe uses eggs. The protein in the egg whites works similar to gluten (which is a protein) to make fluffy muffins. To decrease the eggy flavor, cream cheese is added. I use cream cheese, sour cream or yogurt in many baked goods to neutralize eggy flavors.

 

 

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Keto Lemon Poppyseed Muffins

5 (1) Prep 10m Cook 15m Total 25m 12 servings

Ingredients

  • 1 ¼ cup almond flour
  • 3 tablespoons coconut flour
  • 2 teaspoons baking powder
  • 1/4 teaspoon salt
  • 2 tablespoons poppy seeds
  • 4 tablespoons unsalted butter
  • 4 tablespoons cream cheese
  • 2 tablespoons coconut oil
  • 1/2 cup granulated sugar-free sweetener
  • 1/4 cup sour cream
  • 4 eggs
  • juice and zest from one large lemon or two small lemons
  • 1 teaspoon vanilla extract

Step by Step Instructions

Step by Step Instructions

1
Preheat and prep

Preheat the oven to 350°F. Line a 12-cup muffin tin with paper liners and set aside.

Cupcake liners in a muffin tray.
2
Dry ingredients

Whisk together almond flour, coconut flour, baking powder, salt, and poppy seeds.

A whisk on top of mixed dry ingredients.
Tip Make sure to break up any clumps of almond flour.
Ingredients for this step
  • 1 ¼ cup almond flour
  • 3 tablespoons coconut flour
  • 2 teaspoons baking powder
  • 1/4 teaspoon salt
  • 2 tablespoons poppy seeds
3
Some of the wet ingredients

Add the butter, cream cheese, and coconut oil to a larger microwave safe bowl. Melt in the microwave at 30 second intervals until melted. Whisk until smooth.

Melted butter and oil in a glass dish with a whisk over it.
Ingredients for this step
  • 4 tablespoons unsalted butter
  • 4 tablespoons cream cheese
  • 2 tablespoons coconut oil
4
More wet ingredients

Whisk in the sugar and sour cream until combined. Then whisk in the eggs, lemon juice and zest, and vanilla.

Smooth wet ingredients in a bowl with a whisk on top.
Ingredients for this step
  • 1/2 cup granulated sugar-free sweetener
  • 1/4 cup sour cream
  • 4 eggs
  • juice and zest from one large lemon or two small lemons
  • 1 teaspoon vanilla extract
5
Muffin batter

Slowly sprinkle in the dry ingredients into the wet ingredient and mix until you have a thick batter.

Poppyseed muffin batter in a bowl with a black handled whisk.
6
Time to scoop

Use a large scoop or a ⅓ cup measure to fill the lined muffin cups about ¾ full. You should have enough to fill 10-12 muffin cups.

Muffin batter filled in muffin liners in a pan.
Tip If you like a puffy muffin top, then fill close to the top.
7
Bake

Bake the muffins in the preheated 350°F oven for 15-20 minutes or until the tops of the muffins spring back when touched and a tester inserted in the center comes out clean.

Baked lemon poppyseed muffins in a baking tray.
Tip Let the muffins cool in the muffin pan for a few minutes before removing. Let muffins cool completely before peeling from the liner.
Nutrition Per Serving 1 muffin
194 Calories
17.2g Fat
5.6g Protein
2g Net Carbs
4.2g Total Carbs
12 Servings
Nutrition disclaimer

The nutrition information provided is an estimate and is for informational purposes only. I am a Doctor of Pharmacy (Pharm.D.); however, this content is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always consult your physician or other qualified health provider before making any lifestyle changes or beginning a new nutrition program.

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Keto Lemon Poppyseed Muffins

Frequently Asked Questions

How to you keep the muffin from sticking to the liner?

Besides using high quality muffin liners and muffin pans, spraying the muffin liner with a bit of cooking spray can help prevent the muffin from sticking to the liner. Make sure the muffins cool completely before peeling the liner away as well.

Can butter be used instead of coconut oil?

Yes! More butter can be used instead of coconut oil in this recipe.

How do I keep poppyseeds from getting stuck in my teeth?

It's hard to keep poppyseeds from getting stuck in your teeth, but here's some tips on how to dislodge them. Drink water right away and swish it around. Keep a toothpick or flosser handy.

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Crumbs falling off of a bitten poppyseed muffin.

Best muffin liners & pan

Silicone liners are often praised for being the best muffin liners, but I think they are a pain to store and wash, so I just use paper liners. Not all paper muffin liners are the same. Some stick to the paper. Read reviews before picking up any old muffin liner brand. When it comes to muffin pans, look for a non-stick muffin pan. Wilton makes a decent non-stick muffin pan for a great price. But this USA Muffin Tray is also a favorite.
A stack of lemon poppyseed muffins baked in liners.

Storage information

Before storing the muffins, allow them to cool completely, then put them in either an airtight container or ziploc bag. If you are worried they will stick together, place parchment paper between layers. Store them at room temperature for only a day. Any longer and they may start to dry out. For longer storage, put them in the refrigerator for up to 4-5 days. You can freeze them in a freezer-safe container or bag for up to 3 months. Then pull out one or two at a time to thaw in the refrigerator or room temperature whenever you want a muffin!
About the Author
Annie Lampella, Pharm.D.

Annie Lampella, Pharm.D.

Annie is a Doctor of Pharmacy, mom, and the recipe creator behind KetoFocus. With a B.S. in Genetics from UC Davis, she has over 14 years of experience developing family-friendly keto recipes based on the science of human metabolism.

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  1. M
    Maryanne Jul 31, 2024

    Is there a substitute for cream cheese? Like avocado oil mayonnaise or a healthier fat?

    1. Annie Lampella
      Annie Lampella May 5, 2025

      I haven't tried any substitutions, so I'm not how well these will work, but you could try blended cottage cheese, greek yogurt or ricotta cheese. I'd may say 1/3-1/2 cup.

  2. K
    Kerri Apr 17, 2024

    Amazing!! Perfect recipe, thank you!

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