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Pumpkin Chocolate Chip Protein Muffins – Easy Cream Cheese Swirl Recipe

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These pumpkin chocolate chip protein muffins with a tangy cream cheese swirl are moist, satisfying, and packed with protein—perfect for breakfast, meal prep, or a cozy fall snack. They combine classic autumn flavors with a healthy twist and freeze beautifully for busy mornings.

Ingredients

Scale
  • 1 cup (245g) canned pumpkin puree (not pumpkin pie mix)
  • 2 large eggs, room temperature
  • 1/2 cup (120ml) unsweetened almond milk (or dairy milk)
  • 1/3 cup (80ml) avocado oil or melted coconut oil
  • 1/2 cup (100g) coconut sugar or light brown sugar
  • 1 tsp vanilla extract
  • 1 cup (120g) white whole wheat flour (or all-purpose flour)
  • 1/2 cup (40g) vanilla or unflavored protein powder (whey, plant-based, or collagen)
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 1 1/2 tsp ground cinnamon
  • 1/2 tsp pumpkin pie spice (or extra cinnamon)
  • 2/3 cup (120g) mini chocolate chips
  • 4 oz (113g) cream cheese, softened (regular or light)
  • 2 tbsp (30ml) maple syrup or honey
  • 1/2 tsp vanilla extract (for cream cheese swirl)

Instructions

  1. Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper or silicone liners, or grease if not using liners.
  2. In a large bowl, whisk together pumpkin puree, eggs, almond milk, oil, coconut sugar, and vanilla extract until smooth and creamy.
  3. In a separate bowl, whisk together flour, protein powder, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice.
  4. Add the dry ingredients to the wet ingredients and stir gently until just combined. Do not overmix.
  5. Fold in the mini chocolate chips, reserving a few for topping if desired.
  6. In a small bowl, beat the softened cream cheese, maple syrup, and vanilla extract until smooth and creamy.
  7. Divide the muffin batter evenly among the 12 muffin cups (about 3/4 full).
  8. Drop a heaping teaspoon of the cream cheese mixture on top of each muffin. Use a toothpick or knife to gently swirl the cream cheese into the top layer of batter.
  9. Bake for 18-22 minutes, or until a toothpick inserted into the muffin (not the cream cheese) comes out mostly clean.
  10. Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. Store leftovers in the fridge for up to 5 days or freeze for up to 2 months.

Notes

Do not overmix the batter to keep muffins tender. Use room temperature eggs, milk, and cream cheese for best results. For gluten-free, use a 1:1 gluten-free flour blend. For dairy-free, use plant-based cream cheese and chocolate chips. Muffins freeze well and taste even better the next day as flavors meld. Add nuts or swap chocolate chips for seasonal variations.

Nutrition

Keywords: pumpkin muffins, protein muffins, chocolate chip, cream cheese swirl, healthy breakfast, fall baking, meal prep, high protein, easy muffins, gluten-free option