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Pumpkin Cream Cheese Muffins Recipe

If you’re looking for a fall treat that feels like a warm hug in muffin form, my Pumpkin Cream Cheese Muffins Recipe is exactly what you need. I absolutely love how these muffins come out tender and moist with that perfect pumpkin flavor, all crowned by a luscious cream cheese swirl that just melts in your mouth. It’s one of those recipes that works brilliantly for breakfast, snack time, or even a cozy dessert with a cup of coffee.

When I first tried this Pumpkin Cream Cheese Muffins Recipe, I was amazed at how simple ingredients and a straightforward process could create something so impressive. You’ll find that the balance of spices with the richness of pumpkin and cream cheese topping makes these muffins stand out from your typical pumpkin baked goods. Trust me, your family will go crazy for these — they’re a total crowd-pleaser!

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Why You’ll Love This Recipe

  • Perfectly Balanced Flavors: The pumpkin spices and cream cheese swirl create a delicious contrast that keeps it exciting in every bite.
  • Simple Ingredients: Using pantry staples with canned pumpkin means you can whip these up quickly anytime inspiration strikes.
  • Versatile for Any Occasion: Great for breakfasts, snacks, potlucks, or even a holiday dessert—you’ll never regret baking a batch.
  • Fun to Customize: Whether you want to add nuts or turn these into mini muffins, there’s room to make this recipe your own.

Ingredients You’ll Need

I love how this recipe combines white whole wheat and unbleached all-purpose flour for a tender crumb with a touch of wholesome goodness. Plus, the pumpkin pie spice mix perfectly complements the natural sweetness of the pumpkin puree.

  • White Whole Wheat Flour: Adds a nutty flavor and more fiber than regular flour.
  • Unbleached All-Purpose Flour: Helps keep the muffins light and fluffy.
  • Raw Sugar: Gives a subtle molasses flavor that pairs beautifully with pumpkin.
  • Baking Soda: This is your leavening agent for rise and fluffiness.
  • Pumpkin Pie Spice: The star blend of cinnamon, nutmeg, and more spices, creating warmth.
  • Nutmeg and Cinnamon: Added individually to boost those classic pumpkin flavors.
  • Salt: Balances sweetness and enhances all the other flavors.
  • Canned Pumpkin: Not pumpkin pie filling—pure pumpkin puree is the secret for moist texture.
  • Coconut Oil: Provides healthy fats and helps keep the muffins moist.
  • Egg: Binds everything together and adds structure.
  • Vanilla Extract: A splash of vanilla enhances all the flavors.
  • Cream Cheese: The creamy, tangy topping that makes these muffins extra special.
  • Additional Raw Sugar: Mixed into the cream cheese for just the right amount of sweetness.
  • Egg Yolk: Helps give the cream cheese swirl a silky texture.
Note: You’ll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Variations

One of the things I love most about this Pumpkin Cream Cheese Muffins Recipe is how easy it is to tweak according to your preferences. You can make it gluten-free, nutty, or even turn it into bread — the possibilities are endless, and each twist brings a new delight.

  • Gluten-Free Version: While I haven’t personally tried this, I’ve heard great things using a 1:1 gluten-free baking flour like Cup4Cup — if you try it, please share how it goes!
  • Add Nuts: My family loves when I toss in some chopped walnuts or pecans for extra crunch and flavor.
  • Use Different Oils: If you don’t have coconut oil, you can substitute with melted butter or a neutral oil like canola — I’ve tested both, and they work just fine.
  • Mini Muffins: Perfect for parties — just reduce the baking time to about 20 minutes and use a mini muffin pan for bite-sized treats.

How to Make Pumpkin Cream Cheese Muffins Recipe

Step 1: Prep Your Oven and Muffin Tin

Start by preheating your oven to 350°F. Line your muffin tin with paper liners and give them a quick spray with baking spray to prevent sticking—this simple step makes cleanup and muffin removal painless. I usually line up everything first to keep things moving smoothly once I start mixing.

Step 2: Mix the Dry Ingredients

In a medium bowl, whisk together the white whole wheat flour, all-purpose flour, raw sugar, baking soda, pumpkin pie spice, nutmeg, cinnamon, and salt. Using a wire whisk here helps evenly distribute the spices and baking soda, which is key to a uniform rise and flavor in the muffins.

Step 3: Combine the Wet Ingredients

In a large bowl, mix the canned pumpkin, melted coconut oil, one large egg, and vanilla extract. I like to use a hand mixer just until thick and creamy—don’t overbeat, just enough to combine well. Scrape the sides of the bowl to catch any pumpkin that might be clinging on.

Step 4: Bring It Together

Slowly add the dry ingredient mix to the pumpkin mixture and gently blend on low speed until everything just comes together. This is where you want to be careful not to over-mix, or your muffins could turn out dense instead of fluffy — a few lumps are totally okay!

Step 5: Prepare the Cream Cheese Swirl

In a separate bowl, beat the cream cheese until smooth, then gradually add two tablespoons of raw sugar, the egg yolk, and vanilla extract. Mix until it’s silky with no lumps left. This creamy swirl is what really elevates these muffins to the next level—trust me, you don’t want to skip this step.

Step 6: Build Your Muffins and Swirl

Spoon the pumpkin batter into your prepared muffin liners, filling each about three-quarters full. Drop about one tablespoon of the cream cheese mixture on top of each muffin. Grab a toothpick and gently swirl the cream cheese into the batter — moving carefully from the edge toward the center to create a pretty marbled effect.

Step 7: Bake and Cool

Place your tin on the oven’s center rack and bake for 24 to 26 minutes. Use the toothpick test here: poke it into the center, and if it comes out clean (or with just a few moist crumbs), your muffins are ready. Let them cool for a bit before digging in. I promise, the wait is worth it because these muffins are best when not piping hot but still warm.

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Pro Tips for Making Pumpkin Cream Cheese Muffins Recipe

  • Look for Canned Pumpkin, Not Pie Filling: Using pure pumpkin puree avoids extra sugars and spices for better control over flavor.
  • Don’t Overmix the Batter: A few lumps are okay—overworking the flour can toughen your muffins.
  • Swirl Gently for a Pretty Effect: Use a gentle hand and a toothpick to get those beautiful swirls without mixing the cream cheese fully into the batter.
  • Use Room Temperature Ingredients: This helps everything combine smoothly, especially cream cheese, so you get that silky swirl.

How to Serve Pumpkin Cream Cheese Muffins Recipe

A close-up view of a muffin with a rough, uneven surface showing swirls of light beige and dark brown layers mixed through the top. The muffin sits in a crinkled, light beige paper liner that stretches outward in soft folds, placed on a white marbled surface. Other similar muffins are partially visible around the main one, all in matching paper liners. The light reflects softly off the swirled texture of the muffin, highlighting its moist and uneven top. photo taken with an iphone --ar 4:5 --v 7

Garnishes

I usually keep these muffins simple, but sometimes I sprinkle a little extra cinnamon sugar on top right after baking, which gives a lovely slight crunch and extra flavor. If I’m serving guests, a dollop of whipped cream or a drizzle of maple syrup really makes it feel special.

Side Dishes

These Pumpkin Cream Cheese Muffins pair beautifully with a hot latte or chai tea, especially as a cozy autumn morning breakfast. I also like serving them alongside a fresh fruit salad for a bright contrast, or with a simple green salad if I’m making them for brunch.

Creative Ways to Present

For holiday parties, I like to arrange mini pumpkin cream cheese muffins on a tiered stand, decorating the platter with little cinnamon sticks and autumn leaves. They also make adorable gifts—wrapped in parchment and tied with twine, they feel just as thoughtful as they taste.

Make Ahead and Storage

Storing Leftovers

I store leftover muffins in an airtight container at room temperature for up to two days. They stay surprisingly moist and flavorful, but if you want to keep them longer, refrigeration is your friend. Just let them come back to room temp before serving for the best texture.

Freezing

I’ve had great success freezing these muffins individually wrapped in plastic wrap and then placed in a freezer bag. They freeze nicely for up to three months, making them perfect for meal prep or whenever pumpkin craving strikes out of season.

Reheating

When I reheat, I unwrap and warm the muffins in a 300°F oven for about 10 minutes or use a few seconds in the microwave. This gently revives their softness and melts the cream cheese swirl just a bit for that fresh-baked feeling.

FAQs

  1. Can I use fresh pumpkin instead of canned pumpkin in this Pumpkin Cream Cheese Muffins Recipe?

    Yes, you can, but you’ll need to cook and puree the fresh pumpkin first to get that smooth, moisture-rich consistency similar to canned pumpkin. Also, fresh pumpkin sometimes has a milder flavor, so the spices might need a little extra boost. I find canned pumpkin the easiest and most reliable, but fresh pumpkin works well if you prepare it properly.

  2. How do I prevent the cream cheese swirl from sinking to the bottom?

    Great question! The key is to drop the cream cheese mixture carefully on top of the filled batter and then gently swirl just a bit—don’t overmix into the batter. Also, make sure your batter isn’t too thin; a thicker batter helps keep the cream cheese suspended near the top during baking.

  3. Can I make this recipe vegan?

    While I haven’t tried a vegan version yet, you can experiment by substituting the egg with a flax or chia egg, using vegan cream cheese alternatives, and swapping the coconut oil with a plant-based oil. If you give it a shot, let me know how it turns out—I’d love to hear your tips!

  4. What’s the difference between this Pumpkin Cream Cheese Muffins Recipe and regular pumpkin muffins?

    The main difference is the creamy, tangy swirl of cream cheese on top, which adds a delightful texture and flavor contrast. It turns simple pumpkin muffins into a slightly decadent treat that feels special whether for a casual snack or a festive occasion.

  5. Can I add nuts or chocolate chips to this recipe?

    Absolutely! Adding chopped walnuts, pecans, or even chocolate chips is a great way to add texture and extra flavor. I usually toss them into the dry ingredients before combining with the wet — just be sure not to overload, so your muffins still bake evenly.

Final Thoughts

This Pumpkin Cream Cheese Muffins Recipe has become a go-to in my kitchen during the fall—and honestly, any time I want that cozy pumpkin vibe. It’s easy enough to whip up on a lazy weekend morning but impressive enough to serve to friends and family. If you want a homemade treat that feels like a warm cuddle on a chilly day, you really can’t go wrong with these muffins. I hope you enjoy baking (and eating!) them as much as I do.

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Pumpkin Cream Cheese Muffins Recipe

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.5 from 289 reviews
  • Author: Nora
  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Total Time: 40 minutes
  • Yield: 12 muffins
  • Category: Baking
  • Method: Baking
  • Cuisine: American
  • Diet: Low Fat

Description

These Pumpkin Cream Cheese Muffins are moist, flavorful, and perfect for fall or year-round indulgence. They combine the warm spices of pumpkin pie spice with a creamy, tangy swirl of reduced-fat cream cheese for a delicious treat that’s easy to make and perfect for breakfast, snacks, or dessert.


Ingredients

Dry Ingredients

  • 1/2 cup white whole wheat flour (King Arthur)
  • 3/4 cup unbleached all-purpose flour (King Arthur)
  • 3/4 cup raw sugar
  • 1 teaspoon baking soda
  • 2 teaspoons pumpkin pie spice
  • 1/4 teaspoon nutmeg
  • 1/4 teaspoon cinnamon
  • 1/4 teaspoon salt

Wet Ingredients

  • 1 1/2 cups canned pumpkin (not pumpkin pie filling)
  • 2 tablespoons coconut oil
  • 1 large egg
  • 1 1/2 teaspoons vanilla extract

Cream Cheese Swirl

  • 5 oz 1/3 less fat cream cheese
  • 2 tablespoons raw sugar
  • 1 large egg yolk
  • 1 teaspoon vanilla extract

Other

  • Baking spray (for muffin tin liners)


Instructions

  1. Preheat and Prepare Muffin Tin: Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners and lightly spray each liner with baking spray to ensure easy muffin removal.
  2. Mix Dry Ingredients: In a medium bowl, whisk together the white whole wheat flour, all-purpose flour, raw sugar, baking soda, pumpkin pie spice, nutmeg, cinnamon, and salt until fully combined. Set aside.
  3. Combine Wet Ingredients: In a large bowl, mix the canned pumpkin, coconut oil, whole egg, and vanilla extract. Beat at medium speed until the mixture is thick and smooth. Scrape down the sides of the bowl to incorporate all ingredients evenly.
  4. Add Dry Ingredients to Wet: Gradually add the flour mixture into the wet pumpkin mixture. Blend at low speed just until combined; avoid overmixing to keep the muffins tender.
  5. Prepare Cream Cheese Swirl: In a separate large bowl, beat the cream cheese until smooth. Slowly add in raw sugar, egg yolk, and vanilla extract, beating continuously until the mixture is combined and creamy.
  6. Assemble Muffins: Pour the batter evenly into the prepared muffin tin. Drop about 1 tablespoon of the cream cheese mixture onto the top of each muffin. Using a toothpick, gently swirl the cream cheese from the edges towards the center, creating a marble effect.
  7. Bake: Place the muffin tin on the center oven rack and bake for 24 to 26 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  8. Cool and Serve: Allow muffins to cool in the tin for a few minutes before transferring to a wire rack to cool completely. Serve warm or at room temperature.

Notes

  • Sugar: Raw sugar can be substituted with granulated white or brown sugar based on preference.
  • Flour: You may use all white whole wheat flour or all-purpose flour depending on availability.
  • Gluten-Free Option: Try using a gluten-free flour blend like Cup4Cup if gluten-free is needed; results may vary.
  • Spices: If pumpkin pie spice isn’t available, substitute by mixing cinnamon, nutmeg, ginger, cloves, and allspice.
  • Add Nuts: Chopped walnuts or pecans can be added to the batter for extra texture and flavor.
  • Oil Substitute: Coconut oil may be swapped for any other neutral oil you prefer.
  • To Make Pumpkin Bread: Pour batter into a loaf pan and bake for about 50 minutes. Test doneness with a toothpick.
  • Mini Muffins: Use a mini muffin tin and one teaspoon of cream cheese topping per muffin. Bake for approximately 20 minutes at 350°F.

Nutrition

  • Serving Size: 1 muffin
  • Calories: 170 kcal
  • Sugar: 16 g
  • Sodium: 160 mg
  • Fat: 6 g
  • Saturated Fat: 4 g
  • Unsaturated Fat: 2 g
  • Trans Fat: 0 g
  • Carbohydrates: 25 g
  • Fiber: 2 g
  • Protein: 3.5 g
  • Cholesterol: 34 mg

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