Gluten-Free Cheesecake Cupcakes


Coming from a family that has a lot of gluten intolerance, I decided to try and come up with a gluten-free cheesecake cupcake recipe that everyone can enjoy. I've tried many different recipes and finally came up with one that I love, and I hope you all love it, too! It tastes great plain or topped with whipped cream, chocolate ganache, fruits, and more - the options are endless. Happy baking!

Prep Time:
15 mins
Cook Time:
32 mins
Additional Time:
2 hrs 20 mins
Total Time:
3 hrs 7 mins
12 mini cheesecakes


  • cooking spray


  • 1 cup gluten-free flour blend (such as Namaste Perfect Flour Blend)

  • 1 cup chopped pecans

  • 7 tablespoons butter, melted, or more as needed

  • ¼ cup packed brown sugar


  • 3 (8 ounce) packages cream cheese, at room temperature

  • cup sugar, or more to taste

  • teaspoon salt

  • 3 eggs

  • 1 ½ teaspoons vanilla extract

  • ½ teaspoon lemon extract, or more to taste


  1. Preheat oven to 350 degrees F (175 degrees C). Grease a muffin tin with cooking spray.

  2. Mix flour, pecans, butter, and brown sugar together in a bowl until mixture has a sandy texture. Drop a heaping tablespoon of the mixture into the bottom of each muffin cup; press to create a flat and even crust.

  3. Bake in the preheated oven until crust is dry, about 12 minutes. Reduce oven temperature to 300 degrees F (150 degrees C).

  4. Beat cream cheese in a large bowl with an electric mixer on low speed until very creamy. Add sugar and salt; mix well. Beat in eggs one at a time until smooth. Beat in vanilla extract and lemon extract.

  5. Pour cream cheese mixture evenly over each crust.

  6. Bake cheesecakes in the preheated oven until set, about 20 minutes. Let cool completely, about 20 minutes. Cover and refrigerate until firm, at least 2 hours.

Cook's Note:

Substitute lemon zest for the lemon extract if desired.

Nutrition Facts (per serving)

442 Calories
35g Fat
27g Carbs
8g Protein
Nutrition Facts
Servings Per Recipe 12
Calories 442
% Daily Value *
Total Fat 35g 45%
Saturated Fat 18g 88%
Cholesterol 126mg 42%
Sodium 257mg 11%
Total Carbohydrate 27g 10%
Dietary Fiber 2g 8%
Total Sugars 17g
Protein 8g
Vitamin C 0mg 1%
Calcium 64mg 5%
Iron 1mg 7%
Potassium 133mg 3%

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

** Nutrient information is not available for all ingredients. Amount is based on available nutrient data.

(-) Information is not currently available for this nutrient. If you are following a medically restrictive diet, please consult your doctor or registered dietitian before preparing this recipe for personal consumption.

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