Pumpkin Chocolate Chip Muffins with Cream Cheese Filling and Streusel

These pumpkin chocolate chip muffins are layered with a thick cheesecake filling and big bittersweet chocolate chips, then crowned with a cinnamon streusel that stays crunchy thanks to one egg white. A hot start in the oven gives them tall, bakery-style tops.

Ingredients for Pumpkin Cream Cheese Muffins

This recipe has four parts: pumpkin batter, homemade pumpkin spice mix, cream cheese filling, and crunchy cinnamon streusel. Full amounts are in the recipe card below.

Pumpkin Batter

• Pumpkin puree: One 15 oz (425 g) can. Use plain pumpkin puree, not pumpkin pie filling, which is already sweetened and spiced. If your puree is very wet, add up to 1 tablespoon more flour.
• Greek yogurt: Plain, full-fat Greek yogurt adds moisture and a little tang, so the batter needs only ¼ cup of oil.
• Avocado oil: Any neutral vegetable oil works.
• Eggs: 4 large eggs for structure.
• Vanilla bean paste: For vanilla flavor with visible flecks.
• Brown sugar: Whisked into the wet ingredients until it dissolves.
• All-purpose flour, baking soda, and salt.
• Bittersweet chocolate baking chips: Large baking chips, not minis, for bigger pockets of chocolate. Reserve about ⅔ cup for the tops.

Homemade Pumpkin Spice Mix

• Cinnamon, ginger, allspice, nutmeg, and clove: The homemade blend adds up to 2½ tablespoons.
• Store-bought swap: Use 2½ tablespoons of pumpkin pie spice instead.

Cream Cheese Filling

• Cream cheese: A full pound, softened. That’s twice what most pumpkin cream cheese muffin recipes use, which is why the filling shows up as a thick layer in every bite.
• Egg: 1 large egg.
• Sugar and flour: ¼ cup sugar and 1 tablespoon flour.
• Milk: A tablespoon; water works too.

Crunchy Cinnamon Streusel

• Egg white: The key to a streusel that stays crunchy and doesn’t melt into the muffin, so don’t leave it out.
• Melted butter, flour, brown sugar, cinnamon, and a pinch of salt.

How to Make Pumpkin Chocolate Chip Muffins with Cream Cheese and Streusel

1. Prep. Preheat the oven to 425°F and take the cream cheese out to soften. Grease the muffin pan with butter.

2. Mix the spice blend. Stir together the cinnamon, ginger, allspice, nutmeg, and clove, or measure 2½ tablespoons of store-bought pumpkin pie spice.

3. Whisk the wet ingredients. In a large bowl, whisk the eggs, pumpkin puree, Greek yogurt, oil, vanilla bean paste, and brown sugar until the sugar dissolves.

4. Add the dry ingredients. In a medium bowl, mix the flour, baking soda, salt, and spice blend (not the chocolate chips). Add it to the wet ingredients and mix until well combined. The batter should be thick; if your puree was very wet, add up to 1 tablespoon more flour.

5. Make the cream cheese filling. In a small bowl, beat the softened cream cheese, sugar, flour, egg, and milk with an electric mixer or whisk until smooth and lump-free.

6. Make the streusel. In another small bowl, mix the flour, melted butter, brown sugar, cinnamon, egg white, and salt. Don’t skip the egg white; it’s what makes the topping crunchy.

7. Layer the muffins. Set aside about ⅔ cup of chocolate chips for the tops. Fill each cup with alternating layers of pumpkin batter, chocolate chips, and cream cheese filling.

8. Top with streusel and chips. Break the streusel into pieces of different sizes with your hands and pile them on each muffin. Press the reserved chocolate chips into the streusel.

9. Bake hot, then lower the heat. Bake at 425°F for 6 to 7 minutes, then lower the oven to 350°F and bake 13 to 14 minutes more. They’re done when a toothpick comes out clean and the streusel is golden brown.

See the rise in the muffins? That comes from the high initial oven temperature. The heat creates what bakers call “oven spring,” the increase in volume you get during the first few minutes of baking. Starting hot and then lowering the temperature is what gets you taller muffins.

10. Cool. Let the muffins cool in the pan until you can lift them out, then move them to a cooling rack to cool completely. Refrigerate any you won’t eat within 2 hours.

How to Store Pumpkin Cream Cheese Muffins

Because of the cream cheese filling, store these in the refrigerator, not on the counter.

• Room temperature: Refrigerate within 2 hours of baking. Plain muffins are fine on the counter, but dairy fillings change the rules. The USDA says soft cheeses like cream cheese, yogurt, cheesecake, and cream-filled pastries shouldn’t be kept above 40°F for longer than 2 hours, and it specifically excludes baked goods with cream cheese fillings from the muffins that are safe at room temperature.
• Refrigerator: Up to 5 days in a zip-top bag or airtight container.
• Freezer: Up to 1 month.
• Reheating: Warm in a 325°F oven, loosely covered with foil, for 8 to 10 minutes from the fridge or 15 to 20 minutes from frozen. Uncover for the last 2 to 3 minutes to crisp the streusel back up. For a single muffin, the microwave works too: heat in 15 to 20-second bursts until warmed through.

Variations

Instead of Bittersweet Chocolate Chips:

Bittersweet chips give the most contrast against the sweet pumpkin and cream cheese, but any of these work:

• Dark chocolate chips
• Milk chocolate chips
• White chocolate chips
• Cinnamon chips
• Butterscotch chips

Flavor Variations for the Streusel Topping:

Mix any of these into the streusel for a different crunch or flavor:

• Chopped nuts: walnuts, almonds, peanuts, cashews, or macadamias
• Old-fashioned oats (not quick or instant oats)
• Cocoa nibs
• Cocoa powder
• Extra pumpkin spice

Frequently Asked Questions

If you love this combination of pumpkin, chocolate, and cream cheese, it also comes in loaf form: my pumpkin chocolate chip bread with cream cheese swirls is easy to slice and share. For a holiday dessert, try my pumpkin cheesecake or these mini pumpkin layer cakes. If you bake with sourdough, my soft pumpkin sourdough bread brings pumpkin to your bread basket too. And for more ways to cook with Japanese pumpkin, browse my kabocha squash recipes.

I hope these become your favorite fall muffins. If you bake them, leave a rating and a comment below and let me know which chips you used.

Happy baking!