Marbled Chocolate Pumpkin Muffins

These pumpkin and chocolate muffins are absolutely stunning with their beautiful marbled effect, and they’re surprisingly easy to make! The combination of spiced pumpkin batter swirled with rich chocolate creates muffins that look bakery-worthy but come together quickly in your own kitchen.

I love baking muffins and have been sharing my favorites on this site (we’re up to over a dozen recipes and counting!). My daughter is my biggest muffin fan and loves being my little taste tester, which makes developing new muffin recipes even more fun. These chocolate pumpkin muffins got my daughter’s thumbs-up of approval and have quickly became one of our fall favorites because they taste as good as they look.

If you’re anything like me, you lean into pumpkin season and probably have at least two open jars of pumpkin puree floating around in the fridge from September through November (it’s basically a requirement for fall baking, right?!). These muffins are a fun twist on traditional pumpkin muffins that brings chocolate into the mix for something a little more special, and they’re a delicious way to use up that open can of pumpkin.

Ingredients for Chocolate and Pumpkin Muffins

• Salted butter. Adds rich flavor and keeps the muffins tender and moist.
• Canned pumpkin puree. Provides moisture, natural sweetness, and that classic fall pumpkin flavor and color. Make sure to use pure pumpkin puree, NOT pumpkin pie filling.
• Buttermilk. Creates incredibly tender muffins with a subtle tang that also helps balances the sweetness.
• Large eggs. Bind everything together and provide structure while adding richness to the batter.
• Brown sugar AND granulated sugar. The combination adds sweetness with the brown sugar contributing a subtle molasses flavor that complements the pumpkin and fall spices.
• All-purpose flour. Provides the right amount of structure for tender, fluffy muffins without being crumbly or falling apart.
• Baking soda AND baking powder. Used as our leavening agents, working together to give these muffins their nice rise and fluffy texture.
• Salt. Enhances the other flavors and balances the sweetness.
• Ground cinnamon AND pumpkin pie spice. Classic fall spices that make these muffins taste like the season.
• Unsweetened cocoa powder. Gets mixed into half the batter to create the chocolate batter for marbling.
• Semi-sweet mini chocolate chips. Add pockets of melty chocolate throughout the chocolate portion of the muffins and amp up the chocolate flavor too.

All ingredient measurements and full recipe details can be found in the recipe card at the bottom of the page.

Helpful Equipment

You’ll need a standard 12-cup muffin tin and muffin liners (or cooking spray). Two mixing bowls are essential since you’ll be dividing the batter to create the chocolate and pumpkin portions. A butter knife or skewer is perfect for swirling the batters together to create that marbled effect.

How to Make Cocoa Pumpkin Muffins

Prep. Preheat your oven to 375°F and line a standard 12-cup muffin tin with muffin liners (or grease / spray with cooking spray). Set aside.

Mix wet ingredients. Add the melted butter, pumpkin puree, buttermilk, eggs, granulated sugar, and brown sugar to a large mixing bowl.

Whisk together until well combined.

Slowly add the dry ingredients. Whisk in the baking soda, baking powder, cinnamon, pumpkin pie spice, and salt.

Then slowly add in the flour, mixing until JUST combined (a few streaks of flour are ok at this point, don’t overmix for the best texture).

Divide batter in half by transferring half of the batter to a separate medium-sized mixing bowl.

Begin to stir in the cocoa powder.

Then mix in the mini chocolate chips until combined (try not to overmix!!).

Fill the muffin liners with alternating spoonfuls of each batter, overlapping the colors a bit.

Continue until the muffin tins are about ¾ full and the batter has been used up.

If desired, gently drag a knife through the top layer of the batters 2-3 times to “swirl” the batters (the chocolate batter will feel a bit thicker) and top with extra mini chocolate chips.

Bake for 18-22 minutes until a toothpick inserted into the center comes out clean (a few crumbs are ok). 

Let the muffins cool in the pan for a few minutes, then transfer to a wire rack to cool completely.

Pumpkin Chocolate Swirl Muffins Variation Ideas

• Regular milk substitute. If you don’t have buttermilk on hand, you can use regular whole dairy milk instead (we’ve done this!). The muffins will still be delicious, but they won’t be quite as tender or tangy.
• Dark chocolate version. Use dark cocoa powder and dark chocolate chips for a more intense chocolate flavor.
• Cream cheese swirl. Add dollops of sweetened cream cheese to the batter along with the chocolate for an extra decadent version.
• Spice it up. Add a pinch of ground ginger to the pumpkin batter for more complex spice notes.

How to Store Pumpkin and Chocolate Muffins

Store completely cooled muffins in an airtight container at room temperature for up to 3 days. The pumpkin keeps them naturally moist, helping them to stay fresh.

For longer storage, keep them in the refrigerator for up to one week. They’re delicious cold, but you can also warm them in the microwave for 15-20 seconds to bring back that fresh-baked taste and texture.

These muffins also freeze beautifully for up to 3 months. Wrap fully cooled individual muffins with saran wrap or simply place them into a freezer-safe container and store in the freezer. When ready to enjoy, thaw at room temperature when you’re ready to enjoy them, or warm from frozen in the microwave for 30-45 seconds.

Chocolate Pumpkin Muffins Recipe FAQs

Can I use pumpkin pie filling instead of pumpkin puree? No, stick with plain pumpkin puree rather than pumpkin pie filling. Pumpkin pie filling has added sugars and spices that will throw off the recipe’s balance and make your muffins too sweet.

Why did my marble effect disappear? This usually happens from over-swirling the batters. Remember, just 2-3 gentle swirls with your knife is enough! If you swirl too much, the batters blend together and you lose those distinct chocolate and pumpkin sections.

Can I make these without buttermilk? Yes, you can substitute regular whole milk, though the taste is a smidge different and texture won’t be quite as tender (but they are still delicious!! We’ve made them this way and still enjoyed them very much).

How do I know when the muffins are done? When a toothpick is inserted into the center of a muffin it should come out clean or with just a few moist crumbs (not covered in wet batter). The tops should also spring back lightly when touched and look set rather than look shiny or wet.