Keto Lemon Blueberry Muffins
Published October 25, 2020 • Updated February 28, 2026
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I make these keto lemon blueberry muffins with a moist almond flour crumb, fresh blueberries in every bite, and a sugar-free lemon glaze that reminds me of something from a coffee shop. They're a family favorite for breakfast or afternoon snacks.
I’ve been baking these lemon blueberry muffins since I first started experimenting with keto baking, and they’re one of the recipes my family actually requests. Not because they’re ‘healthy’ (my kids don’t think about that), but because the muffin tops puff up golden and the crumb stays soft for days. I’ve made hundreds of batches at this point and the recipe hasn’t changed in years because it just works.
The combination of almond flour and coconut flour gives you a texture that’s closer to regular muffins than anything else I’ve tried. I tested a bunch of ratios before I landed on this one. Too much coconut flour and they get dense and dry. Too much almond flour and they’re crumbly. This blend holds together, stays moist, and actually tastes like a muffin, not a science experiment.
What makes these different from other keto muffins is the fat structure. Butter, coconut oil, and cream cheese together create a crumb that’s tender without being greasy. The cream cheese does something specific here: it neutralizes that coconut and almond flour flavor so you taste lemon and blueberry, not nuts. I’ve made versions without the cream cheese and the almond flavor takes over. If you’ve tried other low carb muffins that taste like almond paste, this is the fix.
The sour cream is another thing I won’t skip. It adds moisture, but more importantly, the acid reacts with the baking powder to give you that puffy muffin top that actually domes up over the liner. If you don’t have sour cream, Greek yogurt works the same way.
I use fresh blueberries because they hold their shape better, but frozen work too. One tip I picked up after a lot of messy batches: toss the blueberries in a tablespoon of coconut flour before folding them in. It keeps them from sinking to the bottom and prevents the batter from turning blue. Small step, big difference.
If you love this flavor combination, try my keto lemon poppyseed muffins for a different take on the lemon crumb. For more low carb breakfast baking, my keto chocolate zucchini muffins and Starbucks keto pumpkin cream cheese muffins use similar techniques. And if you want something outside the muffin family, almond flour pancakes are my go-to weekend breakfast.
How to make keto lemon blueberry muffins
- Combine dry ingredients – Whisk the almond flour, coconut flour, baking powder, and salt together in a small bowl.
- Cream the fats – Melt the coconut oil, butter, and cream cheese together, then mix until smooth. I microwave mine in 30-second bursts.
- Mix the wet ingredients – Stir in powdered sweetener and sour cream, then beat in the eggs, vanilla, lemon juice, and lemon zest.
- Combine wet and dry – Fold the dry ingredients into the wet mixture until just combined.
- Add blueberries – Toss fresh blueberries in a tablespoon of coconut flour first (keeps them from sinking), then fold them into the batter.
- Bake – Fill muffin liners almost to the top and bake at 350 degrees for 17-20 minutes.
- Glaze – Mix powdered sweetener with fresh lemon juice and drizzle over the warm muffins.
Key ingredients and substitutions
- Almond flour and coconut flour – I’ve tested a lot of low carb flour combos, and this one gives you the closest texture to regular muffins. The almond flour keeps things moist while the coconut flour absorbs excess liquid and adds structure. Both are easy to find at most grocery stores.
- Butter and coconut oil – Using both fats together makes these muffins moist and spongy without being greasy. I’ve tried all-butter versions and they’re good, but the coconut oil adds a lightness I prefer.
- Cream cheese – This is the secret ingredient. It neutralizes the nutty flavor from the almond flour and the egg taste, so all you get is lemon and blueberry. Don’t skip it.
- Powdered sweetener – I use powdered sugar-free sweetener because it dissolves completely into the batter. Granulated sweetener leaves a gritty texture. Look for one that measures cup for cup with regular sugar.
- Sour cream – Does double duty here. It adds moisture and the acid reacts with baking powder to help the muffins rise. I’ve swapped in Greek yogurt and it works the same way.
- Eggs – Four eggs give these the structure they need to puff up and hold that perfect domed muffin top.
- Fresh lemon – Juice and zest from one lemon. The zest is where most of the lemon flavor lives. If you’re allergic to zest (I’ve had readers ask), substitute a teaspoon of lemon extract and add an extra tablespoon of juice.
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Keto Lemon Blueberry Muffins Ingredients
1 ¼ cup almond flour -
3 tablespoons coconut flour
-
2 teaspoons baking powder
-
¼ teaspoon salt
-
4 tablespoons unsalted butter
-
4 tablespoons cream cheese
-
2 tablespoons coconut oil
-
½ cup powdered Swerve, or sweetener of choice
-
¼ cup sour cream
-
4 eggs
-
juice and zest from one lemon
-
1 teaspoon vanilla extract
-
1 cup blueberries
Lemon Glaze Ingredients
-
juice from one lemon
-
1 cup powdered Swerve, or sweetener of choice
Step by Step Instructions
Step by Step Instructions
Preheat
Preheat oven to 350 degrees. Place muffin liners in a 12 cup muffin pan.
Mix dry ingredients
In a small bowl, combine almond flour, coconut flour, baking powder and salt. Set aside.
- 1 ¼ cup almond flour
- 3 tablespoons coconut flour
- 2 teaspoons baking powder
- ¼ teaspoon salt
Cream the fats
In a medium bowl, add butter, cream cheese and coconut oil. Melt in the microwave at 30 second intervals until softened. Mix until smooth. Use a hand mixer if needed to blend until smooth.
- 4 tablespoons unsalted butter
- 4 tablespoons cream cheese
- 2 tablespoons coconut oil
Stir in
Stir in powdered sugar free sweetener and sour cream.
- ½ cup powdered sugar free sweetener
- ¼ sour cream
Add eggs and lemon
Beat in eggs, vanilla and juice and zest of one lemon.
- 4 eggs
- 1 teaspoon vanilla
- juice & zest from lemon
Add the dry ingredients
Stir in dry ingredients to the wet mixture.
Now the blueberries
Fold in blueberries.
- 1 cup blueberries
Add to muffin tin
Scoop the muffin tin lined with muffin liners. Fill until you almost reach the top. Bake at 350 degrees for around 17-20 minutes or until muffin has risen.
Lemon glaze
To make the lemon glaze, combine powdered sweetener and juice from one lemon in a small bowl. If you need to thin it out, add more lemon juice. Drizzle on top of muffins.
- 1 cup powdered sugar free sweetener
- juice from one lemon
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 freeze these muffins and reheat them later?
I freeze these all the time and they hold up well. Wrap each muffin individually in plastic wrap, then put them in a freezer bag. They'll keep for up to 2 months. To reheat from frozen, I microwave one for 25-30 seconds or put it in a 300 degree oven for about 8 minutes. The crumb stays moist, though the top won't be as crispy as the day you baked them. I'd skip the glaze before freezing and drizzle it on fresh after reheating. If you're into batch baking, my keto pecan pie muffins freeze just as well.
Why did my muffins stick to the liners?
I had this same issue early on. Let them cool fully in the muffin tin for at least 15 minutes before peeling. The butter content makes them stick when they're warm, but they release clean once they hit room temperature. I don't spray my liners and they come out fine every time, as long as I'm patient enough to wait.
Can I use raspberries instead of blueberries?
I've made these with raspberries and they're great. The flavor leans more tart, which I actually like with the lemon. Raspberries are also lower in carbs than blueberries, so the macros improve a little. Just fold them in gently since raspberries break apart easier than blueberries do. A few of my readers swear by the raspberry version. If you love berry muffins, my keto strawberry muffins are worth trying too.
Can I make mini muffins with this recipe?
I've made both sizes and the mini version is great for snacking or packing in lunches. Use mini muffin liners and fill them almost to the top, same as regular. Reduce the bake time to 10-12 minutes and check them at 10. They're done when the tops spring back when you press lightly. This recipe makes about 24 mini muffins. I still use liners for the minis since they stick even more than the full-size ones.
Can I skip the lemon zest and use lemon extract instead?
I've had readers with citrus zest allergies ask this, and yes it works. Use about 1 teaspoon of lemon extract in place of the zest and add an extra tablespoon of lemon juice. The flavor will be a little less bright than fresh zest (zest has oils that extract can't fully replicate), but it still tastes distinctly lemony. I've tested both ways and the texture stays identical.
Are blueberries okay to eat on keto?
I use blueberries in moderation and they fit my macros fine. One full cup has about 17.8 grams of net carbs, which sounds like a lot, but this recipe spreads that cup across 12 muffins. That's roughly 1.5 grams of net carbs from the blueberries per muffin. I don't stress over it. If you're tracking closely, frozen blueberries sometimes have slightly different counts on the package, so weigh them if that matters to you.
Can I make these dairy free?
I've tested a dairy-free version and it works. Swap the butter for ghee (or more coconut oil), replace the cream cheese with coconut cream, and use dairy-free yogurt instead of sour cream. You lose a little of that tender richness from the cream cheese, but the muffins still come out moist and the lemon flavor actually pops more without the dairy softening it. The glaze is already dairy free as written.
What can I substitute for almond flour if I have a nut allergy?
One of my readers, Dawn, has a severe tree-nut allergy and made these with cauliflower flour in place of almond flour and arrowroot flour in place of coconut flour, plus ghee instead of coconut oil. She said they still came out fluffy and tasty. I haven't tested that exact combo myself, but sunflower seed flour is another swap I've seen work well in keto baking. Start with a 1:1 substitution and adjust if the batter feels too wet or too dry.
Started freezing the blueberries for about 20 minutes before folding them in and the batter doesn't turn purple anymore, which was my whole issue with every other muffin I'd made. They stay mostly whole through baking so you actually get a real blueberry in each bite instead of vague blue streaks throughout. I also swapped the sour cream for full-fat Greek yogurt because that's what I had on hand, and the crumb came out so tender I second-guessed whether they were done when the timer went off (they were). The lemon glaze is where I kept losing track of time, kept going back for 'just one more taste' while trying to drizzle it evenly, which is not a complaint exactly, more of a warning. Next time I'm adding extra zest directly into the glaze and making a double batch because these are moving faster than I planned for.
Freezing the berries first, why haven't I tried that. I've just accepted the purple streaks and moved on. Yes on the extra zest in the glaze, way more lemon.
Brought these to my neighbor's spring brunch and one of her friends pulled me aside to ask what bakery they came from. I had to tell her I made them, which turned into this whole conversation about almond flour because she genuinely didn't believe me. The lemon glaze is what does it, I think. It looks completely legit.
First time baking with almond flour and I'm a little nervous about it. Do these come out dense like some keto muffins I've tried, or does the cream cheese actually keep them light and fluffy?
These aren't dense. The cream cheese and sour cream together keep the crumb really tender, and four eggs give them actual lift. Mine come out closer to a coffee shop muffin than the usual keto brick.
This is my fourth time making these and I finally cracked it. Bottled lemon juice was the problem. Fresh zest and juice makes the kitchen smell incredible when they come out, and the glaze actually tastes like something. The almond and coconut flour combo gives them a crumb that holds together way better than most keto muffins I've tried. Blueberries stay juicy, centers don't get soggy. Docking a star because it took a few rounds to dial in the lemon level, but I've been making a batch every other Sunday. Not planning to stop.
Yeah, bottled lemon just doesn't have the oils from the zest. The glaze especially needs real lemon to taste like anything. Every other Sunday sounds about right.
My daughter has this unspoken rating system where she takes one bite of whatever I bake and quietly goes back to what she was doing. She ate two of these before her coffee this morning and then came back for a third around 11. That is high praise in this house from someone who skips breakfast on principle. What I noticed making them: the sour cream is doing real work in that batter. The crumb came out soft but it holds when you pick it up without a wrapper, which almost never happens with almond flour baking. My one note is the lemon glaze is pretty runny right out of the bowl, so if you want that thicker coffee shop drizzle, add a bit more powdered Swerve than the recipe calls for. Four stars because of that, but the flavor hit exactly what I was going for.
Three before noon counts. The sour cream thing you noticed is exactly it, that plus cream cheese keeps the crumb from going dry like most almond flour bakes do. On the glaze, yeah, runny straight out of the bowl is normal. Add an extra tablespoon of Swerve and it thickens in about two minutes.
I've been burned by keto muffins enough times that I almost didn't bother. The almond and coconut flour combo actually works here, way better crumb than anything I've attempted before. Mine baked a little uneven (my oven runs hot) but the lemon glaze saved them and now I'm just annoyed it took me this long to try this one.
325 next time if your oven runs hot. Check at 14 minutes. The glaze covers a lot of sins but it shouldn't have to.
Toss the blueberries in a tiny bit of almond flour before you fold them in. First batch mine all sank straight to the bottom and I thought I messed up the batter. Second batch, berries in every single bite.
Ha, that batter panic is real. I was sure I messed up something the first time mine all sank. The flour coat fixes it.
My daughter asked me to make these for her school breakfast - she never touches anything lemon. The glaze won her over though. She scraped every last bit off the muffin liner.
Ha, the glaze gets people every time. Even my kids who claim to hate lemon will scrape it clean.
Made these last weekend and every single blueberry sank to the bottom. Just folded them in like normal, fresh out of the container. Should I toss them in almond flour first or something?
Yeah, toss them in a teaspoon of almond flour first. It gives them something to grip in the batter instead of just sinking through.
I've tested at least four keto lemon blueberry muffin recipes looking for one that doesn't taste like sweetened almond flour, and this is the first one that actually delivers. The cream cheese and sour cream together give it this genuinely tender crumb, not the dense wet texture I kept hitting everywhere else. The lemon glaze is so good it tastes like you squeezed a real lemon on top. I'm not looking anymore.
Four recipes worth of blueberries to get here. The sour cream is actually what fixes the dense wet texture - it lightens the crumb in a way cream cheese alone can't.
First time making muffins from scratch and I was a little nervous, but these came out so fluffy and moist. The lemon flavor really pops. One question though - mine stuck to the liners a bit. Should I spray them first or just let them cool longer before peeling?
Let them cool fully in the tin before peeling, like 15 minutes. The butter content makes them stick when they're warm but they release clean once they're room temp. I don't spray mine.
Thank you for posting this recipe, absolutely amazing! The blend of the flours helps with the texture of the almond flour and the cream cheese gives a great background flavor. My husbands a diabetic and it's tough finding recipes that'll work for him that also taste good.
The cream cheese was kind of the whole point for me. That richness keeps them from tasting like almond flour baked into a shape. 3.5g net carbs per muffin, so they're easy to fit in.
I recently got diagnosed with gestational diabetes and I was craving some muffins. I have one as a snack with a bit of double cream on top! Delicious!
Double cream on top is not a bad idea. 3.5g net carbs each so the snack math works out.
Question... these sound wonderful but I am allergic to Lemon "Zest" I can have lemon extract, lemon juice, lemon stevia just cannot have the zest itself. how should I alter your recipe so I can make these...
You could use either. I don't think it needs to be altered, just add it in and taste until you like the flavor.
Add 1/2 tsp of citric acid (powdered Vitamin C you can buy at any health food store) and you will get that great lemony zip you are looking for!
OMG!!!! Okay I'm starting off on keto--only been on it for a little over a week. Was craving something sweet, but have not cheated in terms of eating anything that I'm not allowed. On top of it, I have a really bad tree-nut allergy (I can have peanuts but NOT coconut with my particular allergy) so I can't have coconut flour OR almond flour! But, I decided to give your recipe, with 3 substitutions a try.
I substituted the coconut oil with ghee (clarified butter)
I used cauliflower flour and arrowroot flour for the almond and coconut (arrowroot being the substitute for coconut, cauliflower flour the substitute for almond)
They STILL came out--Nice, fluffy, and still SOOOO Tasty!!!! next time am going to try substituting sunflower seed flour for the almond but...YAY!!!!
I have a feeling that I'm going to be trying soo many more of your recipes--just so so good! Thank you!!!! I was scared to try keto because of my allergy, but I'm slowly, but surely, finding ways around it!!!:)
Your swap is in the FAQ now (cauliflower + arrowroot + ghee). That's what I point people to when someone messages me about nut allergies on this recipe. Sunflower seed flour is on my list to test too.