Keto Lemon Poppy Seed Muffins

These keto lemon poppy seed muffins are soft, tender, and bursting with bright lemon flavor. Made with almond flour, cream cheese, fresh lemon juice, and poppy seeds, they have all the flavor of classic lemon poppy seed muffins without the sugar, gluten, or high carbs.

If you love a bakery-style muffin but want to keep things low-carb, this recipe is such a treat.

The combination of cream cheese and butter gives these muffins a rich, moist crumb, while the lemon juice, lemon extract, and fresh lemon zest add that fresh citrus flavor that pairs beautifully with poppy seeds.

These muffins are perfect for breakfast, brunch, meal prep, or as a sugar-free afternoon snack with a cup of coffee or tea.

I have an entire collection of keto muffin recipes you may want to check out.

Why You'll Love These Keto Lemon Poppy Seed Muffins

There is something so refreshing about the combination of lemon and poppy seeds. It's bright, slightly tangy, and just sweet enough to feel like a treat without being overpowering.

These low-carb lemon poppy seed muffins are:

• Low in carbs
• Sugar-free
• Gluten-free
• Made with almond flour
• Tender and moist
• Full of fresh lemon flavor
• Great for breakfast or snacking
• Easy to make ahead

They are also a great recipe to keep in the refrigerator or freezer when you want a quick keto-friendly option ready to go.

Keto Poppy Seed Muffins

These muffins are made with almond flour instead of regular wheat flour, making them naturally gluten-free and low in carbs. Since almond flour has a tender crumb and mild flavor, it works beautifully in keto muffin recipes.

The cream cheese is also key in this recipe. It gives the muffins a richer texture and helps keep them moist, which is important when baking without traditional flour or sugar.

Fresh lemon juice, lemon extract, and lemon zest work together to give these muffins their bright citrus flavor.

The lemon extract helps boost the lemon flavor without adding extra liquid, while the fresh lemon juice and zest keep the flavor tasting natural and fresh.

Ingredients Needed For Low-Carb Lemon Poppy Seed Muffins

Disclosure: Some of the links below are affiliate links, meaning, at no additional cost to you, I will earn a commission if you click through and make a purchase. 

The following is a list of ingredients you will need to bake your poppy seed keto muffins:

• Cream Cheese:Softened cream cheese helps create a moist and tender muffin crumb. It also adds richness and structure to the batter.
• Butter: Unsalted softened butter gives the muffins a classic buttery flavor and helps create a tender texture.
• Eggs: Room temperature eggs help the batter mix more smoothly and give the muffins structure.
• Granulated Sugar Substitute: Use your favorite granulated sugar substitute that measures cup-for-cup like sugar. For a sweeter muffin, you can increase the amount slightly.
• Almond Flour: Finely ground almond flour works best for this recipe. Be sure to measure and sift the almond flour before adding it to the batter for the best texture.
• Lemon Juice: Fresh lemon juice gives these muffins a bright, tangy flavor that pairs beautifully with the poppy seeds.
• Lemon Extract: Lemon extract intensifies the lemon flavor without making the batter too wet.
• Lemon Zest: A little freshly grated lemon zest adds even more citrus flavor.
• Poppy Seeds: Poppy seeds give the muffins their classic look and add a subtle nutty flavor.
• Baking Powder: Baking powder helps the muffins rise.
• Salt: A little salt balances the sweetness and enhances the lemon flavor.

How To Make Keto Lemon Poppy Seed Muffins

To make these muffins, start by preheating your oven to 400 degrees and lining a 12-cup muffin pan with parchment liners. You can also grease the muffin wells well if you are not using liners.

Next, measure and sift the almond flour. This step helps prevent clumps and gives the muffins a lighter texture.

In a large mixing bowl, beat the softened cream cheese and butter together until the mixture is light and fluffy. This helps create a smooth batter and gives the muffins a better crumb.

Add the granulated sugar substitute and mix until well combined. Then add the eggs one at a time, mixing well after each addition.

Stir in the sifted almond flour, salt, baking powder, and lemon zest. Once those ingredients are incorporated, add the lemon juice and lemon extract and beat until the batter is smooth.

Fold in the poppy seeds, then divide the batter evenly among the prepared muffin cups.

Bake the muffins at 400 degrees for the first 5 minutes. Then, without removing the muffins from the oven, reduce the temperature to 350 degrees and continue baking until the muffins are golden and an inserted toothpick comes out clean.

Allow the muffins to cool in the pan for about 10 minutes before transferring them to a baking rack to cool completely.

How To Get Rounded Muffin Tops

Starting the muffins at a higher oven temperature helps give them a nice lift. Baking them at 400 degrees for the first few minutes allows the batter to rise quickly before the temperature is reduced.

After the first 5 minutes, lowering the oven to 350 degrees allows the muffins to finish baking evenly without becoming too brown.

Since keto muffins do not rise the same way traditional wheat-based muffins do, this simple baking method helps create a fuller muffin top.

For best results, be sure to divide the batter evenly among the muffin cups and avoid underfilling them.

Tips For The Best Keto Poppy Seed Muffins

For the best results, make sure your cream cheese, butter, and eggs are at room temperature before mixing. This helps the batter come together smoothly.

Use finely ground almond flour for the best texture. Almond meal is more coarse and can make the muffins heavier.

Sift the almond flour before adding it to the batter. This small step makes a big difference in the final texture.

Do not skip the lemon extract. Fresh lemon juice adds wonderful flavor, but the extract gives the muffins a stronger lemon taste without adding too much liquid.

Let the muffins cool before serving. Like many keto baked goods, the texture improves as they cool.

Sweetener Options

For this recipe, I recommend using a granulated sugar substitute that measures cup-for-cup like regular sugar.

If you prefer a lightly sweet muffin, use the amount listed in the recipe card. For a sweeter, more dessert-like muffin, increase the granulated sugar substitute to ¾ cup.

A monk fruit and erythritol blend, allulose blend. Check out our keto sweetener guide for a more detailed explanation.

Can I Make These Muffins Dairy-Free?

Because this recipe uses both cream cheese and butter, I have not tested it as dairy-free. You may be able to use a plant-based cream cheese and dairy-free butter substitute, but the texture will likely change.

For best results, I recommend making the recipe as written.

How To Store Keto Lemon Poppy Seed Muffins

Store leftover muffins in an airtight container in the refrigerator for up to 5 days.

You can enjoy them chilled, bring them to room temperature before serving, or warm them slightly in the microwave.

These muffins freeze well. Once the muffins have cooled completely, place them in a freezer-safe container or freezer bag and freeze for up to 3 weeks.

For best results, thaw them in the refrigerator overnight or on the counter before serving.

More Poppy Seed Recipes

If you are a fan of poppy seeds you should also try our other poppy seed recipes.

• Keto Poppy Seed Pound Cake
• Keto Poppy Seed Bundt Cake

Tag Us

I sure hope you'll give this recipe a try. When you do, be sure to tag us on Instagram and Facebook. It truly encourages me to keep sharing and perfecting these keto recipes for you.

You can also visit our Amazon Store for some of our favorite keto baking tools, pantry staples, and low-carb recommendations.

Grab Our Books & Recipe App

In case you don't know, we've authored two keto cookbooks, Essential Keto Bread and Essential Keto Desserts, both inspired by your requests over the years.

You can also find even more easy keto recipes for breakfast, lunch, dinner, snacks, and desserts inside the  Fit to Serve Group App on  iOS and Android.

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