Pumpkin Cheesecake Muffins

Some fall mornings just call for something sweet, warm, and soul-soothing. I still remember the first chilly October when I tried a pumpkin cheesecake muffin at my sister’s kitchen counter, steam curling from our coffee mugs and laughter spilling between bites. The tangy swirl of cream cheese tucked into that pumpkin-spiced batter felt like everything autumn should be — comforting, rich, and a little indulgent.

Now, every year as the leaves turn golden and sweaters come out, these pumpkin cheesecake muffins find their way back into my oven. The best part? You don’t have to run to the coffee shop — these are even better than the store-bought kind, and your home will smell like a dream while they bake.

Let’s make memories one bite at a time.

Why You’ll Love This Recipe

These pumpkin cheesecake muffins hit that sweet spot between cozy and decadent. With their spiced pumpkin crumb and creamy, tangy center, they feel like fall in a bite — but they’re just as welcome any time of year.

They’re easy to make and beginner-friendly. No mixer required, no fancy tricks — just real ingredients and a dreamy payoff. Ready in just 35 minutes, they’re perfect for weekday treats or weekend brunches.

What really makes these muffins shine is the contrast. That silky cheesecake center nestled inside a fluffy pumpkin muffin is pure genius. Add a handful of pumpkin seeds for a little crunch, and you’ve got a texture trifecta.

They freeze beautifully too! You can make a batch ahead of time and reheat for a warm, satisfying snack anytime. Whether you’re baking for guests or treating yourself, this recipe won’t disappoint.

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Ingredient Overview

These pumpkin cheesecake muffins are warm, aromatic, and bursting with autumn flavor. You’ll love how every bite blends spiced pumpkin with luscious cream cheese filling.

• Pumpkin Purée: Not pie filling! Just smooth, pure pumpkin for earthy richness and moist texture.

• Vegetable Oil: Keeps the crumb tender and light, ideal for muffins with staying power.

• Brown Sugar + White Sugar: The mix adds depth, caramel notes, and perfect sweetness.

• Pumpkin Pie Spice: That dreamy mix of cinnamon, nutmeg, and cloves brings the fall vibes.

• Eggs & Milk: Bind and soften the batter, while creating structure for perfect domes.

• Cream Cheese: The star of the show in that creamy center — tangy, rich, and unforgettable.

• Pumpkin Seeds: A sprinkle on top adds crunch and a toasty, nutty finish.

• All-Purpose Flour: Keeps the muffin base light but sturdy enough to hold that filling.

Styling Tip: Sprinkle extra pumpkin pie spice and a few extra seeds on top just before baking — it makes the tops beautifully golden and bakery-worthy.

Step-by-step Instructions

Step 1: Preheat and Prep Your Pan

Start by preheating your oven to 375°F. Line a muffin tin with paper liners or lightly grease with nonstick spray. This recipe makes about 14 pumpkin cheesecake muffins, so you may need two pans or bake in two rounds.

Step 2: Make the Pumpkin Batter

In a large bowl, whisk together the vegetable oil, pumpkin purée, granulated sugar, brown sugar, eggs, milk, and vanilla. Stir until smooth and combined. Add flour, pumpkin pie spice, baking soda, baking powder, and salt. Mix gently until no flour streaks remain — don’t overmix!

Step 3: Whip the Cheesecake Filling

In a separate bowl, beat the softened cream cheese with sugar, vanilla, a touch of flour, milk, and salt. It should be creamy but thick enough to dollop. This luscious center is what makes these pumpkin cheesecake muffins unforgettable.

Step 4: Assemble the Muffins

Fill each muffin liner just under halfway with pumpkin batter. Then spoon about 1 tablespoon of cheesecake filling right in the center. Top with another small scoop of batter to mostly cover the cream cheese. Tip: A cookie scoop makes portioning super simple!

Step 5: Add the Topping

In a small bowl, mix pumpkin seeds with a sprinkle of pumpkin pie spice. Gently press a few into the tops of each muffin. They’ll toast up perfectly in the oven and give your pumpkin cheesecake muffins that signature bakery look.

Step 6: Bake to Golden Perfection

Bake for 15–17 minutes or until a toothpick comes out with just a few moist crumbs from the pumpkin layer (avoid hitting the cream cheese center). The tops should spring back slightly when touched.

Step 7: Cool and Enjoy

Let the muffins rest in the tin for 5 minutes, then transfer to a wire rack. They’re delicious warm but even better once the filling sets. You’ll taste the contrast of tender pumpkin and creamy center in every bite.

Now that your muffins are golden, fragrant, and cozy as can be, let’s explore some pro tips and creative variations to make these pumpkin cheesecake muffins your own!

Pro Tips

Use room temperature cream cheese. Cold cream cheese can turn lumpy and hard to blend. For smooth, velvety filling in your pumpkin cheesecake muffins, let it soften at room temp for at least 30 minutes.

Don’t overfill your muffin liners. These pumpkin cheesecake muffins rise beautifully, so aim to fill liners about ¾ full once both batter and filling are added. This prevents overflow and ensures perfect bakery-style domes.

Toast your pumpkin seeds first. For an extra crunchy finish, lightly toast your seeds before adding to the muffin tops. It adds depth and makes your pumpkin cheesecake muffins even more irresistible.

Make them ahead for busy mornings. These muffins freeze well. Simply pop one in the microwave for 20 seconds for a warm grab-and-go breakfast that tastes like fall comfort. You’ll love having pumpkin cheesecake muffins ready when life gets busy.

If you’re looking for other cozy pumpkin bakes, don’t miss our ultra-creamy Pumpkin Fluff for a dip that’s just as dreamy.

Variations

Swap in maple extract. If you love deep autumn flavor, try replacing the vanilla in the batter or filling with maple extract. It transforms these pumpkin cheesecake muffins into a maple lover’s dream.

Try a gluten-free version. Use a 1:1 gluten-free flour blend, and you’ll still get a moist, tender muffin with all the charm of the original pumpkin cheesecake muffins.

Add mini chocolate chips. Sprinkle a few into the pumpkin batter for a delightful twist. Chocolate and pumpkin are surprisingly delicious together, especially in muffin form.

Switch the seeds. If you don’t have pumpkin seeds, sunflower seeds or chopped pecans work beautifully. The topping on pumpkin cheesecake muffins is meant to add texture — so have fun with it!

Inspired to try more seasonal muffin ideas? Our Fall Cooking Easy Pumpkin Muffins is a simple favorite for cozy baking days.

Frequently Asked Questions

Serving Suggestions

There’s something undeniably magical about pairing warm pumpkin cheesecake muffins with your favorite cozy drinks. Enjoy them fresh from the oven with a homemade chai latte or pumpkin spice coffee. They make a delightful addition to a crisp fall brunch alongside fluffy scrambled eggs and a fruit salad. These muffins are also perfect tucked into a school lunchbox or served as an afternoon snack with apple cider. If you’re planning a festive breakfast table, a sweet pairing with our Pumpkin French Toast is a true fall feast. Whether it’s a casual family gathering or a special morning treat, pumpkin cheesecake muffins bring autumn warmth to any table.

Conclusion

These pumpkin cheesecake muffins aren’t just a recipe — they’re a moment of comfort baked into golden paper cups. From the spiced batter to the creamy, sweet filling, every bite wraps you in cozy fall memories. They’re simple to make, easy to share, and wonderfully freezer-friendly. Whether you’re baking a batch for weekend guests or meal-prepping breakfast with a smile, you’ll love how these muffins bring people together. Looking for more seasonal treats to share? Browse our Desserts category for fall favorites that will keep your oven warm and your heart full and And for more delicious behind-the-scenes, don’t forget to follow us on Pinterest, Instagram, or TikTok.

Try these pumpkin cheesecake muffins and let me know how they turn out! Leave a comment below or tag your muffin masterpieces on social media so I can cheer you on. I’d love to see your twists and creations — maybe even a sprinkle of cinnamon sugar or swirl of caramel!

From my kitchen to yours — happy cooking!