Irresistible Vegan Pumpkin Cream Cheese Muffins: Your Ultimate Fall Baking Guide

Embrace the cozy spirit of autumn with these truly irresistible Vegan Pumpkin Cream Cheese Muffins. This delightful recipe expertly marries the warm, spiced notes of pumpkin with a luscious, tangy cream cheese swirl, delivering a flavor and texture combination that’s simply divine. Finished with a sprinkle of crunchy pepitas, these muffins are a testament to the joy of seasonal baking and promise to become a new favorite in your repertoire.

For years, my kitchen has been a haven for pumpkin muffin enthusiasts. I’ve delighted in sharing beloved recipes like classic vegan pumpkin muffins, creative pumpkin banana muffins, and crowd-pleasing pumpkin chocolate chip muffins. However, if you’ve been dreaming of a pumpkin muffin that offers a delightful surprise – a creamy, cheesecake-like bite nestled right in the middle – then these unique pumpkin cream cheese swirl muffins are crafted just for you!

What truly elevates these pumpkin muffins to an extraordinary level is the rich and tangy vegan cream cheese filling. It transforms a humble pumpkin treat into something spectacular, introducing a creamy texture and a bright, zesty flavor that perfectly complements the earthy sweetness of the pumpkin and the warmth of the spices. Each bite feels like a luxurious indulgence, reminiscent of a gourmet pastry you’d savor at a high-end coffee house, perhaps paired with a comforting pumpkin spice matcha latte. They’re perfect for a special breakfast, a delightful brunch, or an afternoon pick-me-up that truly satisfies.

Why You’ll Adore These Vegan Pumpkin Cream Cheese Muffins

• Unmistakable Cozy Pumpkin Spice Flavor: If the arrival of pumpkin spice season fills you with excitement (and let’s be honest, who isn’t guilty?), then these pumpkin cream cheese muffins are about to become your new obsession. The expertly balanced blend of warm, inviting spices—like cinnamon and pumpkin pie spice—melds beautifully with the earthy, sweet notes of real pumpkin puree. It’s a flavor profile that evokes comfort, nostalgia, and all the best feelings of autumn, making these muffins absolutely irresistible for any fall gathering or a simple morning treat.
• Luxurious Tangy Cream Cheese Swirl: The secret weapon in this recipe is undoubtedly the rich, creamy, and wonderfully tangy vegan cream cheese filling. It’s not just a topping; it’s baked right into the heart of each muffin, creating a delightful cheesecake-like texture and a burst of bright flavor that cuts through the sweetness of the pumpkin. This creamy core adds an incredible layer of sophistication and indulgence, making each bite an exciting journey of contrasting yet harmonious tastes and textures. It truly transforms a simple muffin into a gourmet experience.
• Perfectly Vegan with an Easy Gluten-Free Option: We believe delicious treats should be accessible to everyone! This recipe is proudly 100% vegan, made without any animal products, ensuring a compassionate and inclusive option for all. What’s more, adapting these pumpkin cream cheese muffins to be gluten-free is incredibly simple. A straightforward swap of all-purpose flour for your favorite measure-for-measure gluten-free flour blend ensures that those with dietary restrictions can also enjoy these delectable, wholesome muffins without compromising on taste or texture.
• Beautiful Presentation for Any Occasion: Beyond their incredible taste, these muffins boast a stunning appearance with their marbled pumpkin batter and visible cream cheese swirls. Topped with crunchy pepitas, they look as good as they taste, making them perfect for potlucks, brunches, holiday breakfasts, or as a thoughtful homemade gift.

Essential Ingredients for Your Vegan Pumpkin Muffins

Crafting these extraordinary pumpkin cream cheese muffins requires a few key ingredients. Below, we’ll delve into each component, offering tips for selection and substitution to ensure your baking success. For precise quantities and step-by-step instructions, please refer to the detailed recipe card further down.

For the Pumpkin Muffins:

• All-Purpose Flour: The foundation of our muffin structure. For a fantastic gluten-free version of these pumpkin cream cheese muffins, simply substitute with your preferred measure-for-measure gluten-free flour blend. This swap works seamlessly without compromising texture.
• Baking Powder and Baking Soda: These leavening agents are crucial for giving your muffins that perfect fluffy rise and tender crumb. Ensure they are fresh for optimal results.
• Spices (Cinnamon and Pumpkin Pie Spice): The heart of the cozy fall flavor! A generous amount of ground cinnamon pairs with a robust pumpkin pie spice blend to create that classic, warm, and aromatic profile. Feel free to adjust the amounts to suit your personal preference for spice intensity.
• Sea Salt: A pinch of fine sea salt enhances all the other flavors, balancing the sweetness and making the pumpkin and spice notes truly sing.
• Sugar (Brown Sugar, Cane Sugar, or Coconut Sugar): You have flexibility here! Brown sugar adds a lovely molasses note and extra moisture, while cane sugar offers a clean sweetness. Coconut sugar is a great unrefined option that still delivers delicious flavor. Choose your favorite granulated sugar for the muffin batter.
• Pumpkin Puree: This is non-negotiable for true pumpkin flavor! Always make sure you’re buying pure pumpkin puree, not pumpkin pie mix or filling, which contains added sweeteners and spices. Canned pure pumpkin is readily available and convenient.
• Oil (Olive Oil Recommended): A neutral-flavored oil like light olive oil, grapeseed oil, or melted coconut oil adds essential moisture and tenderness to the muffins, keeping them wonderfully moist.
• Nondairy Milk: Any unflavored vegan milk will work beautifully. Almond milk, soy milk, oat milk, or cashew milk are all excellent choices for achieving the right batter consistency.
• Vanilla Extract: A splash of good quality vanilla extract always rounds out and enhances the overall sweetness and depth of flavor in baked goods.
• Pumpkin Seeds (Pepitas) or Oats: These are for topping, adding a delightful textural contrast and a professional finish. Pepitas offer a nutty crunch, while oats provide a rustic chewiness.

For the Cream Cheese Filling:

• Vegan Cream Cheese: The star of the swirl! It’s absolutely vital that your vegan cream cheese is at room temperature before you start mixing. This ensures a smooth, lump-free, and perfectly creamy filling.
• Powdered Sugar (Confectioners’ Sugar): This fine sugar dissolves quickly, creating a smooth and sweet filling with no grainy texture.
• Vanilla Extract: Again, vanilla helps to enrich the flavor of the cream cheese, adding a touch of warmth and aromatic sweetness.

Choosing the Best Vegan Cream Cheese for Baking

When it comes to vegan cream cheese, not all brands are created equal, especially when baking is involved. While some brands are fantastic for spreading on a bagel, they can sometimes become grainy or separate when exposed to oven heat. Through extensive testing, I’ve found that Kite Hill Cream Cheese performs exceptionally well in baked recipes. Its texture remains smooth and creamy, making it my top recommendation for these vegan pumpkin cream cheese muffins and any other baked goods requiring a cream cheese component. Miyoko’s, while delicious, is typically not recommended for baking due as it tends to get grainy.

How to Craft Your Perfect Vegan Pumpkin Cream Cheese Muffins

Creating these delightful vegan pumpkin cream cheese muffins is a straightforward process, broken down into simple steps. Follow along to achieve bakery-quality results right in your own kitchen.

Preparing the Pumpkin Muffin Batter:

• Preheat and Prepare: Begin by preheating your oven to 425°F (220°C). This initial high temperature is key for a beautiful muffin dome. While the oven heats, generously grease your muffin pan or line it with paper liners to prevent sticking.
• Combine Wet Ingredients: In a large mixing bowl, or the bowl of a stand mixer fitted with the paddle attachment, combine the sugar, pumpkin puree, and oil. Beat these ingredients together for about 2 to 3 minutes until the mixture is light and well-combined. Next, incorporate the nondairy milk and vanilla extract, mixing for another minute. Remember to scrape down the sides of the bowl periodically to ensure everything is evenly incorporated.
• Introduce Dry Ingredients: To the wet mixture, add the sea salt, cinnamon, and pumpkin pie spice. Then, sift in the all-purpose flour, baking powder, and baking soda. Sifting is an important step as it removes any clumps and helps to aerate the dry ingredients, leading to a lighter, fluffier muffin.
• Mix the Batter: Begin mixing on a low speed to gently combine the dry and wet ingredients, then increase to medium speed until just incorporated. Be careful not to overmix, as this can lead to tough muffins. The batter should be smooth but don’t worry about minor lumps.
• Portion the Batter: Divide the pumpkin muffin batter evenly among 10 muffin cups. A large cookie scoop or a 1/3 cup measuring cup works perfectly for this, ensuring consistent muffin sizes.

Crafting the Cream Cheese Filling:

• Mix the Filling: In a separate bowl, combine the softened vegan cream cheese, powdered sugar, and vanilla extract. Using a stand mixer or a hand mixer on medium speed, beat these ingredients for about 2 minutes. The goal is a light, fluffy, and completely smooth cream cheese mixture, free of any lumps.
• Pipe the Filling: Transfer the prepared cream cheese mixture into a piping bag. Snip off about a ⅓-inch hole at the tip. Insert the tip of the piping bag into the center of each muffin cup, gently pressing down to create a well. As you squeeze the cream cheese, slowly pull the bag upwards, allowing the filling to create a beautiful swirl on top of each muffin. Aim for approximately 1.5 tablespoons of filling per muffin, distributing it evenly.

Baking and Cooling Your Muffins:

• Top and Hydrate: If desired, sprinkle your chosen toppings—oats or pepitas—over the muffins. Lightly press them into the cream cheese swirl. A vital tip for perfect muffins: fill any empty muffin cups in the pan with a little water. This creates steam in the oven, promoting even baking and a beautifully moist crumb.
• Bake with Two Temperatures: Place the muffin pan into your preheated oven. Bake for 5 minutes at 425°F (220°C). Without opening the oven door, reduce the temperature to 350°F (180°C) and continue baking for another 15 minutes, or until a wooden skewer or toothpick inserted into the center of a muffin comes out clean. This two-temperature baking method helps create that desirable domed top.
• Cool Properly: Once baked, remove the muffins from the oven and allow them to cool in the pan for about 5 minutes. This brief cooling period helps them firm up before transferring. Then, carefully move them to a wire rack to cool completely. Cooling on a rack ensures air circulation, preventing soggy bottoms and maintaining their perfect texture.

Expert Tips for Perfect Pumpkin Cream Cheese Muffins Every Time

Achieving bakery-perfect pumpkin cream cheese muffins is easier than you think with these expert tips:

• Don’t Skip the Water in Empty Muffin Cups: This is a game-changer! Filling any unused cups in your muffin tin with about a tablespoon of water creates steam in the oven. This steamy environment helps the muffins rise beautifully, prevents them from drying out, and ensures a wonderfully moist, even bake throughout the batch. It’s a simple trick that yields professional results.
• Avoid Overmixing the Batter: When combining your wet and dry ingredients, mix just until everything is incorporated. Overmixing develops the gluten in the flour too much, leading to tough, dense muffins rather than the light, tender texture we’re aiming for. A few small lumps in the batter are perfectly fine and often preferred.
• Ensure Room Temperature Cream Cheese for the Filling: This is crucial for a silky-smooth cream cheese swirl. Cold cream cheese will be lumpy and difficult to mix evenly, resulting in a less desirable texture. Plan ahead and let your vegan cream cheese sit out on the counter for at least an hour before you start baking.
• Properly Drain Homemade Pumpkin Puree: If you’re using homemade pumpkin puree instead of canned (which is fantastic if you have the time!), it tends to be higher in moisture. To prevent your muffins from becoming too wet or dense, line a fine-mesh colander with a few layers of paper towels or cheesecloth. Spoon your homemade pumpkin puree into it and let it drain for at least 30 minutes to an hour before measuring and incorporating it into your recipe. This small step makes a big difference in texture. You can find my guide on how to make pumpkin puree here.
• Utilize a Cookie Dough Scoop for Even Muffins: For consistent size and baking time across all your muffins, a large cookie dough scoop or an ice cream scoop is your best friend. It ensures that each muffin cup receives roughly the same amount of batter, leading to an even bake and a uniform presentation.
• Don’t Overfill Muffin Cups: While it might be tempting to maximize muffin size, overfilling can cause them to spill over or bake unevenly. Aim to fill each cup about two-thirds to three-quarters full, leaving enough room for them to rise without overflowing.

Exciting Variations to Elevate Your Muffins

While these vegan pumpkin cream cheese muffins are perfect as is, they also lend themselves beautifully to creative variations:

• Chocolate Chip Cream Cheese Swirl: For the chocolate lovers, fold 1/4 to 1/2 cup of mini vegan chocolate chips into the cream cheese filling before piping. The melted chocolate in the center will be an amazing surprise!
• Decadent Chocolate Drizzle: After the muffins have cooled completely, melt some dark vegan chocolate and drizzle it artfully over the tops. This adds an extra layer of richness and a touch of gourmet flair.
• Butternut Squash Magic: If pumpkin puree is hard to find, or if you simply want to try something new, swap it for canned butternut squash puree. The flavor profile is remarkably similar, offering the same sweet, earthy goodness.
• Nutty Crunch Alternative: Instead of pepitas, top your muffins with finely chopped pecans or walnuts for a different kind of nutty crunch and a deeper, earthier flavor. Toasted nuts will provide an even more intense taste.
• Gingerbread Twist: Add 1/2 teaspoon of ground ginger and a pinch of ground cloves to your pumpkin muffin batter for a delightful gingerbread-inspired flavor.
• Streusel Topping: For an extra layer of texture and sweetness, prepare a simple streusel topping (oats, flour, brown sugar, and vegan butter) and sprinkle it over the muffins before baking, along with or instead of the pepitas.

Delightful Ways to Serve Your Pumpkin Cream Cheese Muffins

These versatile vegan pumpkin cream cheese muffins are fantastic on their own, but they also pair wonderfully with a variety of other dishes. They are perfect for:

• Hearty Brunch Spreads: I love serving these sweet muffins alongside a savory breakfast option. Imagine them with a fluffy tofu scramble, a rich easy vegan quiche, or some crispy tempeh bacon for a balanced and satisfying meal.
• Quick Weekday Breakfasts: For a simple yet fulfilling start to your day, enjoy a pumpkin cream cheese muffin with a side of fresh seasonal fruit or a creamy bowl of homemade vegan yogurt. A glass of non-dairy milk or a cup of coffee makes it complete.
• Afternoon Tea or Coffee Break: These muffins are the ideal companion to your favorite hot beverage. The blend of pumpkin spice and tangy cream cheese complements a warm cup of tea or a robust coffee beautifully, making for a perfect afternoon treat.
• Dessert with a Scoop: Warm a muffin slightly and serve it with a scoop of vanilla bean vegan ice cream or a dollop of coconut whipped cream for an easy, yet elegant dessert.
• Holiday Gatherings: Their festive flavors and beautiful appearance make them a wonderful addition to any Thanksgiving breakfast, Christmas brunch, or fall harvest party spread.

Storing Your Vegan Pumpkin Cream Cheese Muffins

To keep your delicious pumpkin cream cheese muffins fresh and moist, proper storage is key. At room temperature, they will maintain their quality for up to 2 days when kept in an airtight container. For extended freshness, especially due to the cream cheese filling, I recommend storing them in the refrigerator, where they will last for up to a week. Simply bring them back to room temperature or warm slightly before enjoying.

Can I Freeze These Pumpkin Cream Cheese Muffins?

Absolutely! These muffins are freezer-friendly, making them perfect for meal prepping or having a quick treat on hand. Allow the pumpkin cream cheese muffins to cool completely to room temperature before freezing. Once fully cooled, place them in freezer-safe bags or airtight containers. They can be stored in the freezer for up to 3 months without compromising their texture or flavor. When you’re ready to enjoy them, simply thaw overnight in the refrigerator, or for a quicker option, gently warm them in the microwave on low power until they are heated through and soft.

Discover More Delicious Vegan Muffin Recipes

If you’ve enjoyed these pumpkin cream cheese muffins, you’ll love exploring other delightful vegan muffin creations from my kitchen. Each recipe is crafted to be easy, delicious, and satisfying for all palates:

• Bright and Zesty Vegan Lemon Poppyseed Muffins
• Indulgent Double Chocolate Banana Muffins (Vegan & Gluten-Free)
• Wholesome and Moist Vegan Zucchini Muffins
• The Absolute Best Vegan Blueberry Muffins You’ll Ever Make
• Comforting Apple Streusel Muffins with a Crumbly Topping

I hope you thoroughly enjoy these incredible vegan pumpkin cream cheese muffins! If you give this recipe a try, please remember to snap a photo and tag #jessicainthekitchen on Instagram! Your feedback means the world to me, so I’d also be thrilled if you could leave a comment and a rating for the recipe below. Thank you so much for your support and happy baking, friends!

Pumpkin Cream Cheese Muffins

Servings:

10
servings

Prep Time:

10 minutes
mins

Cook Time:

20 minutes
mins

Total Time:

30 minutes
mins

These vegan pumpkin cream cheese muffins pair the cozy flavour of pumpkin with a sweet-and-tangy cream cheese filling with delicious results!

5 (from 3 ratings)

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Ingredients

Pumpkin Muffins

• 2
  cups
  all purpose flour,
  (240g)
• 1
  tablespoon
  baking powder,
  (14g)
• 1/2
  teaspoon
  baking soda,
  (3g)
• 1
  teaspoon
  cinnamon
• 1
  teaspoon
  pumpkin pie spice
• 1/2
  teaspoon
  sea salt
• 1
  cup
  sugar,
  (200g) brown sugar, cane sugar, coconut sugar – any kind of granulated sugar
• 1
  cup
  pumpkin puree,
  (244g) not pumpkin pie filling
• 1/3
  cup
  oil,
  (66g) any oil (I prefer olive oil)
• 1/2
  cup
  nondairy milk + 2 tablespoons,
  (150mL) any vegan milk works
• 2
  teaspoons
  vanilla extract
• 2
  tablespoons
  pumpkin seeds or oats for topping

Cream Cheese Filling

• 8
  oz
  vegan cream cheese,
  room temperature
• 1/4
  cup
  powdered sugar
• ½
  teaspoon
  vanilla extract

Instructions

Pumpkin Muffins

• Preheat oven to 425°F/220°C. Spray a muffin pan with non-stick flour spray or rub with vegan butter, or line with muffin/cupcake liners.
• In a bowl of a mixer or with a hand mixer on medium (or using a whisk), mix the sugar, pumpkin puree and oil together for about 2 to 3 minutes. Add in the milk and vanilla extract and mix together for another minute until fully incorporated, scraping down the sides.
• Into the wet batter add in the sea salt, pumpkin pie spice, cinnamon and then sift the flour, baking powder and baking soda. You want to ensure your flour, baking powder and baking soda are free of clumps so I would recommend sifting them in with a sifter, sieve or a strainer.
• Slowly mix together on low speed, then back to medium, until fully incorporated, for another 2 minutes. Scrape down the sides of the bowl as needed.
• Scoop the muffin batter (I use a large cookie scoop or a 1/3 cup measuring cup) equally into 10 muffin cups/holes.

Cream Cheese Filling

• In a bowl add the softened cream cheese, powdered sugar and the vanilla extract. Using a stand mixer or with a hand mixer or with a whisk, throughly mix all the ingredients together on medium speed until it’s all incorporated and fluffy for about 2 minutes.

Putting it Together and in Oven

• Scoop the cream cheese mixture into a piping bag and cut about ⅓ inch wide hole out. Squeeze the cream cheese down all the way to the tip. To help scoop it into the bag I place my piping bag in a drinking glass to get it as wide open as possible then scoop it in a lot easier.
• Place the tip of the piping bag into the centre of each muffin. Press down to squeeze, pulling up slowly until you reach the top of each muffin. Evenly distribute the batter throughout each muffin, about 1.5 tablespoons in each muffin. Don’t place the bag into the bottom of the batter. When pulling out you can do a little dollop at the top or a swirl.
• If you have any excess batter feel free to push the tip back into the centre of the muffin batter and squeeze some remainder throughout each.
• Add your desired toppings on top of the muffins – I usually do 1 tablespoon oats and 1 tablespoon pumpkin seeds/pepitas, (or 2 tablespoons of only pumpkin seeds or only oats) mix them, then sprinkle them over, pressing in slightly to the top and around the cream cheese hole.
• Place water in the empty muffin cups. Don’t skip this step! It ensures that the muffins bake evenly and rise beautifully
• Add your muffins into the oven. Bake for 5 minutes at 425°F/220°C, then leaving the muffins in the oven and not opening the door, reduce the temperature to 350°F/180°C degrees and bake for another 15 minutes until a toothpick inserted into a muffin comes out clean. Remove from oven and allow to cool in pan for about 5 minutes. Remove (I just use the same toothpick or a knife) and place on a wire rack to cool completely. Allowing the cupcakes to cool completely ensures

Notes

• For the vegan cream cheese, I don’t recommend miyokos for this (it gets grainy) but kite hill cream cheese works incredibly here
• To store: Pumpkin cream cheese muffins will keep for up to 2 days in an airtight container at room temperature, or up to a week in the refrigerator.
• To freeze: You can freeze these muffins for up to 3 months. Allow them to cool completely before placing them in freezer-safe bags or containers. When ready to eat, thaw overnight in the refrigerator or microwave on low power until warmed through.

Calories:
328
kcal

,

Carbohydrates:
48
g

,

Protein:
5
g

,

Fat:
15
g

,

Saturated Fat:
3
g

,

Polyunsaturated Fat:
1
g

,

Monounsaturated Fat:
6
g

,

Trans Fat:
0.001
g

,

Sodium:
394
mg

,

Potassium:
121
mg

,

Fiber:
3
g

,

Sugar:
25
g

,

Vitamin A:
3861
IU

,

Vitamin C:
2
mg

,

Calcium:
116
mg

,

Iron:
2
mg

Disclaimer: Although jessicainthekitchen.com attempts to provide accurate nutritional information, kindly note that these are only estimates. Nutritional information may be affected based on the product type, the brand that was purchased, and in other unforeseeable ways. Jessicainthekitchen.com will not be held liable for any loss or damage resulting for your reliance on nutritional information. If you need to follow a specific caloric regimen, please consult your doctor first.

Cuisine:
American

Course:
Desserts

Author:
Jessica Hylton