Keto Lemon Poppyseed Muffins
Published April 8, 2024 • Updated March 1, 2026
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These keto lemon poppyseed muffins are the fluffiest low carb lemon muffins I've made. Tangy, moist, and ready in about 25 minutes with almond flour and coconut flour.
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. Since I’ve been making keto breakfast recipes for years now, I figured out how to get that same soft, lemony crumb without the carbs. These keto lemon poppyseed muffins are the ones I keep coming back to.
I’ve also made keto lemon blueberry muffins, keto gingerbread muffins, and chocolate zucchini muffins, but this lemon poppyseed version is the one my family grabs first. Something about that combination of bright lemon zest and the little crunch of poppyseeds just works.
What makes these low carb lemon muffins keto?
- Almond flour and coconut flour instead of wheat. I use both together in these sugar free lemon poppyseed muffins because the combination gives you a texture closer to regular all-purpose flour. I’ve tried each on its own and the blend is better.
- Sugar-free sweetener instead of sugar. I look for a combination sweetener (monkfruit plus erythritol, or allulose-based). These measure cup for cup like sugar and actually caramelize slightly on the muffin tops.
- Eggs for structure and lift. Without gluten, you need something to create that fluffy muffin dome. The protein in egg whites does the same job gluten would. I add cream cheese to cut the eggy flavor, and it also keeps the crumb incredibly moist. I use cream cheese, sour cream, or yogurt in a lot of my almond flour recipes for this exact reason.
If you love lemon desserts on keto, try my keto lemon bars or make a glass of keto lemonade to go with these muffins. I do that on weekend mornings and it feels like a real treat.
Tips I’ve learned from making these dozens of times
I’ve made these keto lemon poppyseed muffins more times than I can count, and here’s what I know for sure. Zest the lemon before you juice it. Way easier. I use a microplane and get every bit of that outer rind because that’s where all the lemon flavor lives. The juice adds tartness, but the zest is what makes these taste like real lemon muffins.
Also, don’t overmix the batter. I sprinkle the dry ingredients into the wet and stir just until everything comes together. A few small lumps are fine. Overmixing makes keto muffins dense and tough, and I learned that the hard way with my first batch.
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Ingredients
1 ¼ cup almond flour -
3 tablespoons coconut flour
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2 teaspoons baking powder
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1/4 teaspoon salt
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2 tablespoons poppy seeds
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4 tablespoons unsalted butter
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4 tablespoons cream cheese
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2 tablespoons coconut oil
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1/2 cup granulated sugar-free sweetener
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1/4 cup sour cream
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4 eggs
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juice and zest from one large lemon or two small lemons
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1 teaspoon vanilla extract
Step by Step Instructions
Step by Step Instructions
Preheat and prep
Preheat the oven to 350°F. Line a 12-cup muffin tin with paper liners and set aside.
Dry ingredients
Whisk together almond flour, coconut flour, baking powder, salt, and poppy seeds.
- 1 ¼ cup almond flour
- 3 tablespoons coconut flour
- 2 teaspoons baking powder
- 1/4 teaspoon salt
- 2 tablespoons poppy seeds
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.
- 4 tablespoons unsalted butter
- 4 tablespoons cream cheese
- 2 tablespoons coconut oil
More wet ingredients
Whisk in the sugar and sour cream until combined. Then whisk in the eggs, lemon juice and zest, and vanilla.
- 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
Muffin batter
Slowly sprinkle in the dry ingredients into the wet ingredient and mix until you have a thick batter.
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.
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.
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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Get My Macros + Recipes →Frequently Asked Questions
Can I make these dairy-free?
I haven't done a full dairy-free version myself, but I'd swap the cream cheese for coconut cream and use coconut oil in place of butter. My guess is the texture will be slightly different since cream cheese adds a lot of moisture, but it should still hold together. If you try it, I'd love to know how it turns out.
Can I freeze these muffins?
I freeze these all the time. Once they cool completely, I put them in a freezer bag and they keep for up to 3 months. When I want one, I pull it out the night before and let it thaw in the fridge. By morning it tastes fresh. I've also microwaved a frozen one for about 30 seconds when I forgot to thaw, and that works too.
How do I make these extra fluffy?
I get the fluffiest results when I make sure my eggs are at room temperature before mixing. Cold eggs don't whip up as well. I also sift my almond flour to break up clumps, which makes a real difference in how light the batter is. Some bakers separate their egg whites and beat them stiff before folding in, and I've tried that. It does add extra lift, but honestly my standard method already gives me a nice dome.
Can I use only coconut flour instead of almond flour?
I wouldn't recommend a straight swap. Coconut flour absorbs way more liquid than almond flour, so you'd need to completely rework the ratios. When I've tested coconut-flour-only muffins, I use about 1/3 the amount and add extra eggs and liquid. For this recipe, I really like the blend of both flours because it gives you the best texture. Check out my coconut flour recipes for ones I've built specifically for that flour.
Why did my muffins turn out dense?
I've had this happen and it's almost always one of two things. Either I overmixed the batter (stir just until combined, lumps are fine) or my baking powder was old. I test mine by dropping a teaspoon in hot water. If it doesn't fizz aggressively, I toss it. Also make sure you're measuring almond flour by spooning it into the cup, not scooping directly from the bag. Packed almond flour makes heavy muffins.
Can I substitute the cream cheese?
I got this question from a reader and I've been thinking about it. My best alternatives would be full-fat Greek yogurt, sour cream, or blended cottage cheese. I'd use about 1/3 to 1/2 cup. The cream cheese is there to add moisture and cut the eggy flavor, so you want something with a similar thick, creamy texture. I wouldn't use mayo here since the flavor would be off in a sweet muffin.
How do I keep the muffins from sticking to the liner?
I spray my paper liners with a light coat of cooking spray before filling them. That's the biggest thing that helps. I also make sure the muffins cool completely in the pan before I try to peel the liner off. When I've rushed it and peeled while warm, the top rips off every time. Patience on this one really pays off.
Can I add a lemon glaze to these?
I've done this and it's so good. I mix powdered sweetener (I use Swerve confectioners) with fresh lemon juice, about 2 tablespoons of each, and drizzle it over the cooled muffins. It hardens into a thin sweet-tart shell. My family goes through these faster when I add the glaze, so I save it for weekends when I want something a little extra.
I've been on a lemon kick lately and these are exactly what I want to make this week. I only have light sour cream though, not full-fat. With the cream cheese and butter already in the batter, would it still come out moist or is the full-fat sour cream doing something specific for the texture?
Third batch this month and I'm still just as excited to pull them out. The cream cheese is what does it. That almost bakery-style texture regular muffins just don't have.
Third batch already. The cream cheese is why I never tested a dairy-free version of this one. Too much to lose.
I've tried four or five keto lemon muffin recipes over the past year and the texture was always off. Dense, or just dry by the next day. The cream cheese and sour cream in this batter is what none of the others were doing, and you can taste it immediately. These are actually tangy (not just lemon-scented), and the crumb stays soft without going gummy. This is the one.
Cream cheese gets the credit but the sour cream is the reason it doesn't dry out by day two. Glad you picked up on that.
I've made these at least six times now and the lemon flavor still gets me every time. It's actually bright, not the flat citrus that comes out of most keto baking, and the texture is so much fluffier than I expected from the almond and coconut flour combo. My one note: I wish the poppy seeds came through a bit more, so I've been adding an extra half tablespoon. Not a dealbreaker at all (I've clearly kept making them), but worth the tweak if you want that classic poppyseed flavor up front.
Why combine almond and coconut flour instead of using just one? Trying to understand before I dive in.
Coconut flour absorbs way more liquid than almond flour so they balance each other out. The almond flour carries most of the bulk and fat, and the 3 tablespoons of coconut flour tighten everything up. Try just almond flour and they go flat and greasy.
I swapped the sour cream for full-fat Greek yogurt (I was out) and they came out just as moist, with a slightly brighter lemon flavor. If you're using a dark muffin tin, pull them at 22 minutes because the darker metal runs hot and the edges over-brown before the centers set. I've been making a batch on Sundays and storing them in the fridge, and they're actually better on day two, a little denser and more flavorful. At 2g net carbs each, they're my go-to when I want something that feels like a real treat.
The dark tin tip is really useful. I always test in my light-colored pan so I forget that adjustment. And yeah, day two is genuinely better with these. The crumb tightens up and the lemon flavor gets more concentrated somehow.
Is there a substitute for cream cheese? Like avocado oil mayonnaise or a healthier fat?
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.
Amazing!! Perfect recipe, thank you!
Try drizzling a lemon glaze on the next batch. Two tablespoons Swerve confectioners with fresh lemon juice, let it harden on top. It turns into this thin tart shell.