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Homemade chocolate chip muffins with rich cheesecake filling
Bia

Chocolate Chip Cheesecake Muffins

These chocolate chip cheesecake muffins are soft, rich, and bakery-style with a fluffy chocolate muffin base and a creamy cheesecake center. Every bite gives you a perfect mix of deep chocolate flavor and smooth, tangy filling that melts in your mouth.
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Prep Time 15 minutes
Cook Time 17 minutes
Total Time 32 minutes
Servings: 16 Muffins
Course: Dessert
Cuisine: American
Ingredients Method Notes

Ingredients
  

Cheesecake Filling
  • 8 oz cream cheese softened
  • ½ cup granulated sugar
  • 1 large egg room temperature
  • ½ tsp vanilla extract
  • ¼ cup mini chocolate chips
Chocolate Muffin Batter
  • 2 cups all-purpose flour spooned & leveled
  • ½ cup unsweetened cocoa powder
  • 1 tsp baking soda
  • 1 tsp salt
  • ½ cup coconut oil melted
  • 1 cup granulated sugar
  • 1 large egg room temperature
  • 1 cup plain Greek yogurt
  • ¼ cup milk
  • ¼ cup strong cold coffee
  • 1 tsp vanilla extract
  • ¾ cup mini chocolate chips divided

Method
 

  1. Preheat oven to 400°F (200°C) and line muffin pan with liners.
  2. Beat cream cheese and sugar until smooth.
  3. Add egg and vanilla, mix until creamy.
  4. Stir in mini chocolate chips and chill filling.
  5. Whisk flour, cocoa powder, baking soda, and salt.
  6. In another bowl, mix coconut oil and sugar.
  7. Add egg, yogurt, milk, coffee, and vanilla.
  8. Combine wet and dry ingredients; fold in chocolate chips.
  9. Fill muffin cups halfway with batter.
  10. Add cheesecake filling in center.
  11. Top with remaining batter and chocolate chips.
  12. Bake at 400°F for 5 minutes, then reduce to 350°F for 12–15 minutes.
  13. Cool slightly before serving.

Notes

For the best chocolate chip cheesecake muffins, make sure the cheesecake filling is well chilled before assembling. This helps it stay thick and keeps it from sinking into the muffin batter while baking.
Also, avoid overmixing the muffin batter mix just until the ingredients are combined to keep the muffins soft, fluffy, and bakery-style. Using room temperature ingredients will also help create a smooth batter and even texture.
For the perfect result, don’t skip the two-temperature baking method. The high heat helps the muffins rise quickly, and lowering the temperature ensures they bake evenly inside without drying out.