Looking for the best keto lemon muffins around? These tender cream cheese muffins are easy to make, with a bright luscious lemon flavor. Grain-free!

Spring is springing and lemon recipes are popping up everywhere. And I demand that you put these Keto Lemon Cream Cheese Muffins to the top of your must-make list.
Yep, I absolutely demand it. Because adding cream cheese to your keto muffin batter is a game changer.
I can hear some of you right now: “But Carolyn, you already have a bunch of cream cheese muffin recipes”. And yes, friends, that is correct. There is my ever popular Starbucks copycat Keto Pumpkin Cream Cheese Muffins. And my recently updated Chocolate Cheesecake Muffins.
But while both of those recipes feature a delicious cream cheese center, it’s not in the batter itself. And after my success with Keto Gingerbread Cream Cheese Pound Cake, I found I was eager to try that method again.

Best ever keto lemon muffins?
I am inclined to say yes. I’ve made any number of low carb lemon muffin recipes, but I realized the other day that I don’t have a single one featured here on my blog, as they were all written for other publications.
One of my favorites is the Lemon Ricotta Muffins I created for The Ultimate Guide to Keto Baking. If you love to bake, I cannot recommend my new cookbook enough.
It was time to address the lack of a keto lemon muffin recipe on my site, and after poking around and doing some research, I decided to try them as cream cheese muffins.
Oh my word, I am glad I did! Adding cream cheese to keto muffins gives them both great structure and a rich tenderness that is unparalleled. This may be my new favorite way of making muffins!

How to make keto cream cheese muffins
Darlings, it’s as easy as softening some cream cheese with your butter, and beating them together with the other keto ingredients. But as always, I have some great tips for you to make them perfect.
Room temperature ingredients: You may have seen me mention this before but it’s important. All the beating and creaming of the cream cheese and butter will be for nothing if you add cold eggs. It will clump up and your batter won’t be smooth.
Your choice of sweetener: The muffin batter will be great with any sweetener you like best, as the cream cheese is what provides structure and consistency. You do need a powdered sweetener if you choose to make the drizzle.
Eggs or egg yolks? The egg yolks in this recipe help give these keto lemon muffins a deep rich yellow. If you would prefer, you can use another whole egg instead.
Why protein powder? Oh boy, I get asked this a lot! Simple answer: Gluten is a protein and in its absence, another dry protein powder helps keto baked goods rise and hold their shape. The best sub for whey protein is egg white protein.
Almond flour and coconut flour: I really do love this combination of keto flours and I always use Bob’s Red Mill for both. If you prefer to use only almond flour, you will need an additional 1/4 cup.

Can you make cream cheese muffins dairy-free?
Well, I haven’t tried it myself but I do think you can. Kite Hill almond milk “cream cheese” is an excellent option, and I’ve found it works well in almost all cases. So you should be able to sub that for the cream cheese.
For the butter, you can use coconut oil or another non-dairy oil. If it’s a liquid oil, such as avocado, add it in along with the eggs.
Replace the whey protein with egg white protein powder. Voila! Dairy-free keto lemon muffins.
More keto lemon recipes
- Keto Lemon Cheesecake Bars
- Keto Lemon Poppyseed Bundt Cake
- Easy Keto Lemon Curd
- Low Carb Lemon Ricotta Scones
- Keto Lemon Butter Cookies
- Keto Lemon Coconut Balls

Keto Lemon Cream Cheese Muffins
Ingredients
Lemon Cream Cheese Muffins
- 4 ounces (113.4 g) cream cheese, softened
- 1/4 cup (56.75 g) butter, softened
- 2/3 cup (121.33 g) granulated Swerve Sweetener
- 2 large eggs, room temperature
- 2 large egg yolks, room temperature
- Zest of one lemon
- 1 tsp lemon extract
- 1/2 tsp (0.5 tsp) vanilla extract
- 1 1/2 cups (160 g) almond flour
- 1/4 cup (27 g) unflavoured whey protein powder
- 2 tbsp coconut flour
- 2 tsp baking powder
- 1/4 tsp (0.25 tsp) salt
Lemon Drizzle (optional)
- 1/4 cup (45.5 g) powdered Swerve Sweetener
- 1 1/2 tbsp (1.5 tbsp) freshly squeezed lemon juice
Instructions
Muffins
- Preheat the oven to 350F and line a muffin pan with silicone or parchment liners.
- In a large bowl, beat the cream cheese and butter together until smooth. Beat in the sweetener and then beat in the eggs, egg yolks, lemon zest, lemon extract, and vanilla extract until well combined.
- All at once, add the almond flour, whey protein, coconut flour, baking powder, and salt, and beat until thoroughly mixed.
- Divide the batter among the prepared muffin cups and bake 20 to 25 minutes, until the tops are golden and set to the touch. Let cool completely in the pan.
Drizzle
- In a medium bowl, whisk the sweetener together with the lemon juice until smooth. Drizzle over the cooled muffins.
Video
Nutrition
Nutritional Disclaimer
Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.
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Please can you add the metric conversion to the recipe – I really want to make these muffins but I need to measure ingredients by grams, thanks
Thanks for letting me know it wasn’t turned on.. it is now.
Another great recipe! I loved it! So delicious. Didn’t have lemon extract so I put extra zest like you suggested in the comments. Thank you so much for sharing all the amazing recipes!
Hello ,
I love lemon . I was a little worried because my batter was so thick. However they turned out perfectly. Moist , flavorful .
I love your recipes .
I am so glad! The batter shouldn’t be too thick, though… did you watch the video? It may be that your cream cheese has more thickeners…
Can you use powdered Swerve in place of the granulated in the muffin? Would you measure the powdered in the same amount?
Yes, that works.
Thank you so much! really enjoy your recipes!!!
I made these for my Saturday morning fitness class to celebrate a birthday. I didn’t have time to taste the finished muffins before I offered them to my classmates, but I tasted the batter and was pretty confident they would be delicious. To my pleasure, everyone showered me with compliments and some wanted the recipe. There were 11 of us, and luckily I was able to get an entire muffin to myself. Mmmm, so tasty. The lemon flavor from zest, extract and juice made them perfect for an early Spring post-workout treat, without the guilt. I will definitely make these again, but I’ll add a little more zest because I love lemon. Thanks so much, Carolyn, for sharing this wonderful recipe.
Delighted to hear it!
These muffins sound wonderful, but I’m wondering if there is a substitute for the lemon extract – I have a small kitchen and try not to add things to it that I wouldn’t use very often. Thanks.
Lots and lots of lemon zest and a little lemon juice. It’s the zest that tends to add the most flavor.
I have no protein powder. Is it a must ?
Yup! Please watch this video to understand how protein powder helps baked goods…
https://youtu.be/8SA_iBl0pUU
Can I make this recepy as a cake? How long do I put it in the oven?
I am sure you can but I can’t really guide as to time… you haven’t told me what size pan or anything else.
These are YUMMY!!! Definitely a do-again recipe. Thanks Carolyn, for your wonderful recipes. 🙂
I followed the recipe exactly, and mine came out really dry. I actually choked when I tasted one because it was so dry. The taste is good though. If I make these again, I would not use the coconut flour (ever single time I use coconut flour in anything it turns out so dry), and also I would add more butter and cream cheese.
Something went wrong, then. I can’t say what without more info but these are definitely not dry. Did you use defatted almond flour?
Out of this World. ????????????
Next I want to try a Cranberry/Orange flavor muffin !
These look delicious! Do you know if I could sub THM baking blend for the almond and coconut flours?
What can I say, delicious again! A wonderful recipe, worked the first time without any problems (I halved it), and the only thing I changed was to use your cream cheese frosting (from your carrot cake scones) instead of the lemon drizzle. I loved it (I love cream cheese anything really), and next time I’ll try the lemon drizzle as written in this recipe, just for a more lemony flavour. Thank you, this was a lovely little treat 🙂
So glad to hear it!
Thank you for your free recipes, I love everything you do and trust you with the the ingredients and nutrition you mention
Anything you published I do
And it’s all good
Thank you
Love your blog, thank you for all these delicious recipes
So I had already downloaded your recipe before you fixed the whey protein error and of course, now mine are in the oven without it. ???? I’m hoping they will still taste good but I know now they probably won’t rise how I would like. ???? Fingers crossed!
I’m confused – when did you download it? This recipe has been around for a year and I haven’t touched it in a long time so unless you downloaded it right when it was published and then sat on it that whole time…