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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I am allergic to Whey Powder. Can you please make a recommendation that does not include Whey?
Please read the blog post as I addressed this already! 🙂
Question,
If you wanted to use fresh lemon juice in the muffin recipe, would it be the same amount as the extract?
Thank you,
Deb
No, it won’t be nearly enough to give it lemon flavor. You will need to add more but then offset the wetness by adding more flour.
Thank you! A friend from Phoenix just sent me a big box of freshly picked lemons from her trees. I used every one of these recipes. All of them are delicious!
This is one of my first keto baking recipes attempted and I’m so pleased!! They are just delicious. You would never suspect there is no (wheat) flour in them, great texture and perfectly moist. I didn’t have lemon extract so I used extra zest as you suggested and just a small squeeze of lemon juice. I’m excited to enjoy these for the rest of the week, thank you for making this keto journey so enjoyable!
Great! Welcome to the delicious world of keto baking! 🙂
Carolyn, These are perfect! The texture is light; the flavor delicious and the crumb could be that of a muffin made with wheat flour. I’d give one of these to any keto baked goods skeptic and dare them to turn their nose up. I added blueberries and didn’t make the drizzle. I have lemon oil rather than extract so I use barely 1/8 teaspoon of it. You have outdone yourself, and you’re pretty hard to outdo.
I have a severe food allergy with any and everything coconut. Instead of the 2 tablespoon coconut flour, can I use two more of almond flour?
Is the whey protein necessary in this recipe? I’d prefer not to use it.
It’s always necessary if you want lighter, fluffier muffins. Gluten is a protein and in its absence, another dry protein helps baked goods rise and hold their shape properly.
can I use lemon instead of extract
Do you mean lemon juice? If so…. you need quite a bit of it to get the same lemon flavor, which then changes the liquid content in the batter.
I cannot wait to make these. lemon is my absolute favorite!
Can you use unflavored whey isopure zero carbs protein powder instead of the one you linked? I do t have a Thrive account
Any whey protein powder works.
Thank you
I made these today, and was totally blown away by how incredible they are! I had some fresh blueberries that needed to be used up, so I poked 4 or 5 into each muffin, and the flavors are so light and bright! And the muffins are so moist. Definitely printing this one out to add to my binder so I can make it again…..and again……and again!
I love all of your recipes but this one is my all time favorite!! So light and bright and tender!
Can collagen powder be used as substitute for whey protein powder?
No, it will make them very gummy.
Love this recipe! Making them for the second time today. Planning to freeze this batch (if we can resist eating them). We’re going on a 3 week road trip in our Rv and need sugar free options to hand as I was recently diagnosed with Type 2 diabetes. Your recipes are saving me! Thank you!
I have NEVER liked a keto dessert in all the years I’ve been trying to eat low carb. I tried your earthquake cake a few nights ago and I was in heaven! I figured it had to be a fluke since I’m so picky but I made these muffins last night and they are also to die for! Moist, flavorful and no weird texture or aftertaste! Thank you for these recipes! It opens up a whole new world for me and makes it seem like a keto lifestyle is sustainable and delicious!
Wow… what a lovely comment to receive. I am glad I won you over! 😉
Love these muffins, the lemon flavor is perfect! I’ve made these a few times exactly following the recipe. I made them again yesterday and after mixing all the other ingredients, realized I was out of whey protein and improvised and put in a little extra almond flour until the batter had the right consistency and I have to say the muffins came out fine. The texture is slightly different than if I followed the recipe, but still very good.