Low Carb Keto Cheesecake Cupcakes Recipe
Written by The Protein Chef

Cheesecake cupcakes!!! There’s 2 steps to this recipe and they’re super easy to make.

For your crust, mix together 1/4 cup of almond flour, 1/4 cup of coconut flour, and a tablespoon of coconut oil. Once that’s mixed together add in a tablespoon of melted butter and mix again. Next take out a pan with some silicone cups and press your mix evenly into each one. If you want, throw them in the oven for 10 minutes on 350F/176C to harden up a bit (make them crunchier).

Next add into a bowl 8 ounces of fat free cream cheese, 1 tablespoon of a sweetener, 1 teaspoon of vanilla extract, 1 large whole egg, and 1 scoop of my Baking Protein Powder…which is completely optional. Once it’s smooth distribute it into your cups, top them with whatever you want, and throw them in the oven on 350F/176C for around 15-20 minutes.

Last, you’re gonna let them cool for a bit then wrap them up and throw them in the fridge either overnight or for a couple hours. The silicone cups will make it super easy to remove them once they do cool, seriously a great investment (I’ve had mine for years).

Silicone Cups: http://amzn.to/2mqXyoP

Less than 5 grams of net carbs each and each one is actually pretty filling. The best part? Switch them up by using different flavored protein powders or adding on top fruit, nuts, and so on!

Here is the recipe:

  • 1/4 Cup (28g) Coconut Flour
  • 1/4 Cup (28g) Almond Flour
  • 1 Tablespoon (14g) Coconut Oil
  • 1 Tablespoon Butter (14g)
  • 8 Ounces (240g) Fat Free Cream Cheese
  • 1 Tablespoon Sweetener
  • 1 Teaspoon Vanilla Extract
  • 1 Large Whole Egg
  • 1 Scoop (30g) The Protein Chef’s Baking Protein Powder *Optional

Calories in the WHOLE recipe:

  • Calories: 887
  • Fat: 47g
  • Saturated Fat: 23g
  • Sodium: 958mg
  • Carbs: 46g Net Carbs = 29g
  • Fiber: 17g
  • Sugar: 18g
  • Protein: 70g

Calories in each cupcake (if you make 6):

  • Calories: 147
  • Fat: 7.8g
  • Saturated Fat: 3.8g
  • Sodium: 159.6mg
  • Carbs: 7.6g Net Carbs = 4.8g
  • Fiber: 2.8g
  • Sugar: 3g
  • Protein: 11.6g

How to make:

  1. For your crust mix together your Almond Flour, Coconut Flour, and Coconut Oil
  2. Melt your Butter and mix that in
  3. Distribute your crust mix evenly into the bottom of some silicone muffin cups and press down to compact it
  4. This is an optional step but for harder/crunchier mini crusts you can bake them for 10 minutes on 350F/176C in the silicone cups
  5. Mix together the rest of your ingredients until smooth
  6. Pour that mix into your silicone cups
  7. Bake them on 350F/176C for around 15-20 minutes
  8. Take them out, let them cool, wrap them up, and put them into the fridge for a couple hours (this will give you the perfect cheesecake texture)


  • Top them with some fruit, nuts, or chocolate chips before the oven!

Join Our FREE Recipe Newsletter

Invalid email address

About the author

The Protein Chef

Derek Howes is a personal trainer and chef with over a decade of experience in the gym and kitchen. Derek, who is also known as The Protein Chef on his blog and YouTube channel shows his viewers every week that food doesn’t need to be boring or repetitive, it’s all about balance, moderation, and having the knowledge to change things up. His recipes which have been featured in the news, magazines, and on TV are cheap, quick, AND delicious! His motto in life is “everything in moderation” and is without question the most important habit he follows.


  • Hi there! What you’re doing here with all these recipes is amazing! I can still eat the things I love without the guilt! Quick question for ya. If you only have coconut flour, can you just use that instead or the coconut almond combination? Or will that affect taste and texture?

Leave a Comment