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Keto Lemon Blueberry Muffins

Annie Lampella, Pharm.D. Recipe developer and pharmacist

Published Updated

38 ratings

Coffee shop-style keto lemon blueberry muffins: a moist almond flour crumb, juicy fresh blueberries in every bite, and a sugar-free lemon glaze, all at 3.5g net carbs. They're my family's favorite breakfast or afternoon snack.
  • 3.5gnet carbs
  • 5.4gprotein
  • 30minutes
  • 12servings
three keto lemon flavored muffins with blueberries inside wrapped in a muffin liner
overhead view of blueberry muffins topped with glaze and lemon slices nearby
blueberry muffins in front of a muffin tin without glaze
a stack of muffins in front of a muffin pan
three keto muffins with glaze drizzling down
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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.

Three keto blueberry muffins with fresh blueberries and lemon slices

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.

Three glaze topped blueberry muffins next to whole blueberries and lemon slices.

How to make the lemon glaze

The glaze is just two ingredients: freshly squeezed lemon juice and powdered erythritol. I whisk them together until smooth and drizzle it over the muffins while they’re still a little warm so it sets with that crackly, glossy look. It reminds me of the lemon loaf at Starbucks, that same sweet-tart hit on top of a soft crumb. If the glaze is too thick, add lemon juice a teaspoon at a time. Too thin, add more powdered sweetener. If you love glazed keto pastries, my keto cream cheese danish uses a similar technique.

A closeup of a blueberry muffin topped with a white glaze drizzle.

How to store and freeze these muffins

I store mine in an airtight container at room temperature and they stay soft for 4-5 days. Sugar-free sweeteners don’t hold onto moisture the way regular sugar does, so they’ll start to dry out after that. If you notice them getting a little stiff by day 3, 10 seconds in the microwave brings the texture right back.

These freeze well too. I wrap each muffin individually, toss them in a freezer bag, and they keep for up to 2 months (full details in the FAQ below). My keto banana bread freezes the same way if you like to batch bake on weekends.

How to make keto lemon blueberry muffins

  1. Combine dry ingredients: Whisk the almond flour, coconut flour, baking powder, and salt together in a small bowl.
  2. Cream the fats: Melt the coconut oil, butter, and cream cheese together, then mix until smooth. I microwave mine in 30-second bursts.
  3. Mix the wet ingredients: Stir in powdered sweetener and sour cream, then beat in the eggs, vanilla, lemon juice, and lemon zest.
  4. Combine wet and dry: Fold the dry ingredients into the wet mixture until just combined.
  5. Add blueberries: Toss fresh blueberries in a tablespoon of coconut flour first (keeps them from sinking), then fold them into the batter.
  6. Bake: Fill muffin liners almost to the top and bake at 350 degrees for 17-20 minutes.
  7. Glaze: Mix powdered sweetener with fresh lemon juice and drizzle over the warm muffins.

Ingredients for blueberry muffins in small bowls.

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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The recipe

Keto Lemon Blueberry Muffins

Print Pin
Prep 10 min Cook 20 min Total 30 min Serves 12

Ingredients

Servings 12

Keto Lemon Blueberry Muffins Ingredients

Lemon Glaze Ingredients

Step by Step Instructions

  1. Preheat

    Preheat oven to 350 degrees. Place muffin liners in a 12 cup muffin pan.

    red 350 on a black background

  2. Mix dry ingredients

    In a small bowl, combine almond flour, coconut flour, baking powder and salt. Set aside.

    For this step

    • 1 ¼ cup almond flour
    • 3 tablespoons coconut flour
    • 2 teaspoons baking powder
    • ¼ teaspoon salt
    dry ingredients mixed in a white bowl

  3. 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.

    For this step

    • 4 tablespoons unsalted butter
    • 4 tablespoons cream cheese
    • 2 tablespoons coconut oil
    coconut oil

  4. Stir in

    Stir in powdered sugar free sweetener and sour cream.

    For this step

    • ½ cup powdered sugar free sweetener
    • ¼ sour cream
    butter and cream cheese in a microwave safe bowl

  5. Add eggs and lemon

    Beat in eggs, vanilla and juice and zest of one lemon.

    For this step

    • 4 eggs
    • 1 teaspoon vanilla
    • juice & zest from lemon
    sour cream and swerve in a bowl on top of butter mixture

  6. Add the dry ingredients

    Stir in dry ingredients to the wet mixture.

    wet ingredients for a muffin mixture in a bowl

  7. Now the blueberries

    Fold in blueberries.

    For this step

    • 1 cup blueberries
    dry ingredient on top of wet muffin batter

  8. 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.

    blueberrys in lemon muffin batter in a bowl

  9. 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.

    For this step

    • 1 cup powdered sugar free sweetener
    • juice from one lemon
    lemon muffin batter scooped into muffin tin

Nutrition

Per serving: 1 muffin

Calories
185
Fat
16.2g
Protein
5.4g
Total carbs
5.7g
Net carbs
3.5g

Nutrition is an estimate calculated from the ingredients listed. Brands vary, so check labels if you track closely.

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.

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Reviews

Tap to rate

4.8 from 38 ratings, 24 written

Made this recipe?

Replying to Jasmine

Your rating

Harriet

Bringing these to a brunch Saturday and I want to bake them Friday night so I’m not rushing. Does the glaze hold overnight, or does it sink in and go sticky? I’d rather leave them plain and glaze in the morning if that’s safer.

Reply

Melissa

Let the batter sit a minute before scooping, coconut flour keeps drinking up moisture and it’s way easier to scoop once it firms up. First keto bake for me. Didn’t expect much lift from almond flour but the crumb actually springs back.

Reply

Denise

Don’t mix after the blueberries go in. A few folds, that’s it. I overmixed my first batch and the berries broke apart and turned the whole batter purple. The second time I barely stirred and got intact blueberry pockets instead. Also tried skipping the glaze for weekday mornings, the lemon in the crumb carries them just fine without it. Four stars, would push to five if the glaze set a little thicker.

Reply

Jessica

There’s a slight spring to the crumb you don’t expect from almond flour muffins. The coconut flour does that. Three tablespoons isn’t much but it firms up the structure enough that these hold when you peel the liner back instead of going dense or wet in the middle. Pure almond flour versions fall apart if the ratios are off at all; this one doesn’t.nnThe cream cheese, sour cream, and butter combo is something I hadn’t seen in this ratio before, and it keeps things moist without going heavy or greasy. The lemon lives more in the glaze than the crumb (the crumb is subtler citrus-wise), so if you want more punch you’d bump the zest. Easy fix, not a knock on the recipe.

Reply

Annie Lampella

Lemon in the crumb staying subtle is on purpose. If both the crumb and the glaze were pushing citrus the blueberry would get lost in there. The glaze is where I keep that punch.

Reply

Ashley

3.5 net carbs per muffin and I’m still suspicious I did the math wrong. My 9-year-old walked past the cooling rack and said the glaze looked like something from the coffee shop near school. She doesn’t say that about my baking. New to almond flour, so these were the first batch I’d call actually good rather than just ‘fine for keto.’ The sour cream is doing something real. The crumb stayed soft the next morning. Glaze ran a little thin across all 12, so I’d make extra next time.

Reply

Annie Lampella

The 9-year-old coffee shop comparison made me laugh, Ashley. The math is right on the carbs, the blueberries spread across 12 muffins so each one stays low. The sour cream is the reason the crumb holds up overnight, I’ve made it without and it’s drier and denser.

Reply

Jasmine

Less sweetener on batch six. The lemon actually comes through now.

Reply

Annie Lampella

Six batches and you found it. The zest hides behind too much sweetener, less gives it room.

Reply

Laura

batch five and I’m doubling the glaze every time now

Reply

Laura

Good to know it won’t tip sweet. Full double next time.

Reply

Annie Lampella

I’d double it. I kept it light on purpose because it doesn’t tip sweet, but more is always better here.

Reply

Sarah M.

My grandmother made these every summer. The lemon glaze brought that back immediately. Almond flour gives a denser crumb than hers, but close enough.

Reply

Annie Lampella

The glaze is where the whole thing lives. Crumb will never match wheat flour exactly, but the cream cheese and sour cream together get it closer than a straight almond flour muffin would.

Reply

Andre

Batch four this spring. Finally cracked the storage situation on these. Pop them in the fridge Sunday and by Tuesday they’re actually better. The almond flour crumb gets dense and almost fudgy, and the lemon comes through way more on day two. I’ve been splitting the batch, six with the glaze and six without, because the glazed ones get tacky against each other by day three (small thing, totally worth it). Reheating surprised me too: twenty seconds in the microwave and they come out tasting like they just left the oven. 185 cal, 3.5 net carbs. Genuinely can’t wait for breakfast this week.

Reply

Annie Lampella

Day two is better, you’re not wrong. The lemon blooms more overnight somehow and that crumb gets exactly what you’re describing. I always just stacked mine with parchment and lived with the tackiness.

Reply

Amber

These came out really well but the blueberries sank straight to the bottom of every muffin. Next time I’m going to toss them in a little coconut flour before folding them in, which usually fixes that. That aside, the lemon glaze is worth making alone. The sour cream keeps the crumb from going dense the way a lot of almond flour baked goods do.

Reply

Eric

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?

Reply

Annie Lampella

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.

Reply

Diane

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.

Reply

Annie Lampella

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.

Reply

Rachel

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.

Reply

Annie Lampella

Ha, that batter panic is real. I was sure I messed up something the first time mine all sank. The flour coat fixes it.

Reply

Lindsey

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.

Reply

Annie Lampella

Ha, the glaze gets people every time. Even my kids who claim to hate lemon will scrape it clean.

Reply

Tasha

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?

Reply

Tracy

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.

Reply

Annie Lampella

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.

Reply

Shanya

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!

Reply

Annie Lampella

Double cream on top is not a bad idea. 3.5g net carbs each so the snack math works out.

Reply

Carol

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…

Reply

Annie Lampella Recipe author

You could use either. I don’t think it needs to be altered, just add it in and taste until you like the flavor.

Reply

Ajohnson

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!

Reply

Dawn Tlustachowski

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!!!:)

Reply

Annie Lampella

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.

Reply

Jewel

Thank you so much for this recipe, you have changed my life and I graciously want to thank you. I have needed something like this, I’ve lost 23 pounds and I was stalled, these were absolutely amazing. Thank you so much

Reply

Annie Lampella

23 pounds is huge, congrats. These sit at 3.5g net carbs so they’re my go-to when I need something sweet but can’t mess with macros.

Reply

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