What’s better than a delicious keto chocolate muffin? One with a cream cheese center, of course! Add a few melty chocolate chips on top and you’re in low carb breakfast heaven.
Surely you know by now how much I rely on keto muffins to stick with my health goals. I always have some in the fridge or freezer for easy breakfasts or snacks. I have often credited them with keeping me on track because they’re easy, delicious, and store so well. And the flavor variations are endless!
Sometimes it’s fun to jazz them up a little and take them over the top. These Chocolate Cheesecake Muffins have been one of my favorites for quite some time. How can you go wrong with a rich chocolate base and a creamy cheesecake filling?
While they make an excellent breakfast treat, they are also special enough for dessert.
Reader’s Thoughts
“By far my boyfriends favorite keto dessert I make! It’s gone into regular rotation. Currently making a batch and going to try freezing half of them. Thanks so much for this amazing recipe!!” — Jess
Why You Will Love This Recipe
- Bakery-style: These muffins are worthy of any occasion. They look and taste like they came from your favorite bakery!
- Nut-free option: You can swap out the almond flour for sunflower seed flour, for a nut-free keto treat.
- Make-ahead recipe: Make a big batch and store in the freezer for whenever you need a treat.
- Creamy cheesecake: The cheesecake center is ultra-creamy and decadent.
- Low-carb: This recipe is perfect for low carb, keto, and gluten-free diets.
Ingredient Notes
- Cream cheese: You can’t have a cheesecake center without cream cheese!
- Heavy cream: This helps make the filling extra creamy.
- Almond flour: I typically use almond flour, but sunflower seed flour makes a wonderful nut-free version.
- Cocoa powder: Dutch cocoa powder gives these muffins a rich, deep chocolate flavor.
- Protein powder: This gives the muffins better lift and structure.
- Sweetener: I recommend an erythritol based sweetener for the muffin batter. You can use your preferred sweetener in the filling.
- Heavy whipping cream: This is used to thin out the cream cheese filling.
- Liquid: I like to use leftover coffee but water works as well.
- Chocolate chips: Feel free to use your favorite brand of keto chocolate chips.
- Kitchen staples: Eggs, butter, vanilla extract, baking powder and salt.
How to Make This Recipe
- Prepare the filling: Beat the cream cheese with the sweetener until combined. Mix in the cream and vanilla until smooth.
- Combine the dry ingredients: Whisk the almond flour with the sweetener, cocoa powder, protein powder, baking powder, and salt.
- Add the wet ingredients. Add the eggs, melted butter, coffee, and vanilla extract.
- Assemble the muffins: Divide the batter evenly into muffin cups. With the back of a spoon, create a well in the center of each muffin. Divide the cream cheese filling among the wells and sprinkle chocolate chips on top.
- Bake the muffins. Bake until the edges are set and the centers are puffed up. Remove and let cool in the pan.
Tips for Success
I used chocolate protein powder for this recipe, but you can use plain or vanilla instead. If using vanilla, make sure to leave out the added vanilla extract.
A little coffee enhances chocolate flavors, without making them taste like coffee, so I highly recommend. But plain water is a good option too!
Sweetener Options: I recommend erythritol sweeteners for the muffin batter, as allulose can make the muffins overly browned and taste a little burned. If you wish to cut back on the erythritol, you can try one quarter cup, and use some stevia or monk fruit extract for additional sweetness.
For the cheesecake filling, any kind of sweetener works, as long as it is powdered.
Keto Chocolate Cream Cheese Muffins
Ingredients
Cream Cheese Filling
- 6 ounces (170.1 g) cream cheese, softened
- 1/4 cup (47.5 g) powdered sweetener
- 3 tbsp (45 ml) heavy whipping cream
- 1/2 tsp vanilla extract
Chocolate Muffins
- 1 3/4 cups (196 g) almond flour, (can use sunflower seed meal)
- 1/3 cup (63.33 g) sweetener, erythritol based recommended
- 1/4 cup (21.5 g) cocoa powder
- 1/4 cup (27 g) whey protein powder, or egg white protein powder
- 2 tsp baking powder
- 1/4 tsp salt
- 3 large eggs, room temperature
- 1/3 cup (75.67 g) butter, melted
- 1/3 cup (78.86 ml) coffee or water, room temperature
- 1/2 tsp vanilla extract
- 3 tbsp (45.65 g) dark chocolate chips, sugar-free
Instructions
Cream Cheese Filling
- In a large bowl, beat the cream cheese with the sweetener until well combined. Add the cream and vanilla and beat until smooth. Set aside.
Muffins
- Preheat the oven to 350ºF and line a muffin pan with 12 silicone or parchment muffin liners.
- In a large bowl, combine the almond flour, sweetener, cocoa powder, protein powder, baking powder, and salt.
- Add the eggs, butter, coffee, and vanilla extract and stir until well combined.
- Divide the batter evenly among the prepared muffin cups, filling each no more than 2/3 full. With the back of a spoon, create a well in the center of each muffin.
- Divide the cream cheese filling among the wells, adding about 1 1/2 tbsp to each muffin. Sprinkle the tops of the muffins with chocolate chips
- Bake 20 to 25 minutes, until the edges are set and the centers are puffed up. Remove and let cool in the pan (the centers will rise and sink, this is normal).
Notes
Nutrition
Frequently Asked Questions
If you can find a good cream cheese alternative that you like, you certainly can. Replace the butter with avocado oil and the heavy cream with some coconut cream. Be sure to read the label on the dairy-free cream cheese, as many of them contain more carbs.
Because of the cream cheese filling, I recommend storing these muffins in a covered container in the fridge. Eat chilled or room temperature. You can also freeze them for up to 3 months.
This keto chocolate cream cheese muffins recipe has 7g of carbs and 3.3g of fiber per serving. That comes to 3.7g net carbs per muffin.
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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Can I put half the chocolate mix in and then add the cream cheese mix and top with more chocolate mix
Sure!
Carolyn: I am on my 2nd batch of these delicious Choc Cr Cheese muffins! I took half to our daughter and SIL and EVERYONE raved about them…they are SO good.! Thanks so much for all the delicious recipes! I don’t know what I would do without you!
The consistency of the cake and the cream part were perfect, but they just weren’t sweet enough! I don’t see anyone else saying that, so maybe it’s just me. I love them but would have to add more sweetener to both parts. will be trying again.
Keep in mind that sweetness from alternative sweeteners differs brand to brand, but also palate to palate. Many readers experience my recipes as TOO sweet, so I always take a middle of the road approach. For you, I recommend adding another tbsp or two to each component next time. 🙂
Can I use collagen peptides in place of the protein powder?
Sadly, no. It will make them very gummy and hard to cook through.
Can’t wait to make these! They look so good. Love your recipes and appreciate your sharing them with us.
let’s just say yummy yummy! The chocolate muffin base is similar to the mocha chocolate chip breakfast cookie in Carolyn’s breakfast cookbook- and it’s a serious favorite of mine! this cheesecake topping takes it up another level!
Thanks so much!
how necessary is the whey protein?
They rise much better so pretty necessary.
I used Wellbee Extra Fine almond flour (what I had) and I was very careful about measurements because here in the low-humidity low desert I have trouble with batter and dough consistency. My batter also seemed too runny and I added some more almond flour but it was still nothing like the photos. I couldn’t well up my batter so I just plopped on the cream cheese mix and it sank in just fine.
Is the weight measurement for almond flour the same for sunflower seed flour? It would be nice if all recipes gave the weights as well as the dry measures.
The cream cheese mixture I could eat with a spoon! That stuff is delicious!
Are your eggs larger, by chance? If you were weighing almond flour, you should use about 105g per cup. Same with any nut flour or seed flour.
My eggs could be larger. Thanks for the weight. I notice that I can pack almond flour, and therefore I need to weigh mine to be consistent. These were fantastic! Mine didn’t sink nearly as much (or appeared sunken) as much as the photos show. The cream cheese just floated on top since I couldn’t make a well in the batter. I’ll be making these again.
These muffins are easy and delicious! I used cashew cream cheese, almond milk and plant butter for a friend who can’t have dairy. We both loved them!
Great to hear that you can do them dairy free!
I to be the batter to be a perfect consistency to make the wells. I think my 2 dozen size muffin pan is slightly undersized on the cups as I measured carefully but yielded 4 extra muffins. The 4 that I baked separately rose perfectly and are picture perfect. The 24 with the cheesecake dollops did not rise in the center. Most are very concave and some just spread. I’m sure they are still going to be delicious. Any suggestions on what may have went wrong?
If you check my muffins, they are concave in the center too. That’s the nature of the cream cheese filling! 🙂
So delicious! My family gobbled them up, even the non-keto members. I will be making this recipe often.
Hi, Carolyn,
Batter turned out real runny. Used sunflower seed flour, maybe I ground it too fine? Need to get it done, so using as-is. Would appreciate input for next time.
If it was runny, you simply didn’t have enough flour. Could be mismeasured or could be too “fluffy” after you ground it up. Try weighing it instead. 1 cup of sunflower seed flour should be about 110g.
Greetings,
These looks delish but I don’t consume almond or hemp products. Can coconut milk & coconut flour be substituted to make the muffins? If so, what are the amounts?
No coconut flour is not a good sub for almonds. Try sunflower seed flour.
Delicious – I assume these need to be stored in refrigerator?
Unless you live in a very hot climate, they are okay on the counter for 2 days or so. In the fridge after that!
By far my boyfriends favorite keto dessert I make! It’s gone into regular rotation. Currently making a batch and going to try freezing half of them. Thanks so much for this amazing recipe!!
Great to hear!