Vegan Pumpkin Muffins with Cream Cheese Filling

These vegan pumpkin muffins with cream cheese filling are made with a moist pumpkin batter, a rich, tangy filling and a crunchy pecan streusel topping. They are the perfect fall breakfast treat! Let's learn how to make them.

The perfect muffin has all of the best textures - moist cake, creamy filling and crunchy topping. These vegan pumpkin muffins with cream cheese filling check all the right boxes.

Perfectly spiced and wonderfully festive, this incredibly easy recipe will be added to your regular rotation in no time.

Looking for more breakfast pumpkin munchies? Be sure to check out our vegan pumpkin pancakes and our vegan pumpkin scones.

Muffin Ingredients

You'll need the following ingredients to make perfectly moist and delicious pumpkin muffins:

For the Muffins

• All-purpose flour: Provides structure to the muffins.
• Sugar: Sweetens and helps with browning.
• Baking powder: Leavening agent that makes the muffins rise and stay light.
• Salt: Enhances the flavors and balances the sweetness.
• Spices: Classic pumpkin spice blend adds warmth, depth, and seasonal flavor.
• Pumpkin puree: Moisture, flavor, and natural sweetness; makes muffins tender.
• Nondairy milk: Adds moisture and helps bind the batter.
• Canola oil: Keeps the muffins moist and tender.
• Molasses: Deepens flavor and adds subtle richness and warmth.
• Vanilla extract: Enhances the overall flavor and sweetness.

For the Filling

• Vegan cream cheese: Creates a rich, tangy, and creamy center that mimics traditional cheesecake.
• Light brown sugar: Sweetens the filling and adds a subtle caramel-like depth.
• Vanilla extract: Enhances the sweetness and adds warm, aromatic flavor.
• Cornstarch: Helps stabilize the filling so it holds its shape during baking and prevents it from becoming too runny.

For the Topping

• All-purpose flour: Forms the structure of the streusel so it crisps up nicely.
• Sugar: Sweetens the topping and caramelizes during baking.
• Cinnamon: Adds warmth and complements the pumpkin and pecans.
• Chopped pecans: Provide crunch and nutty flavor contrast.
• Melted vegan butter: Binds the streusel together and helps it brown beautifully.

Why You'll Love These Muffins

• Bakery-style texture - Soft, tender, and perfectly fluffy pumpkin muffin with a creamy center that feels like a professional bakery treat-minus the price tag.
• Fall flavors in every bite - Warm spices like cinnamon and nutmeg plus rich pumpkin purée make these taste like autumn wrapped in a muffin liner.
• Surprise cream cheese filling - The tangy, sweet vegan cream cheese filling melts into a cheesecake-like pocket that balances the sweetness and adds a creamy contrast.
• Completely dairy-free and egg-free - Ideal for anyone avoiding dairy or eggs, yet so delicious no one will guess they're vegan.
• Easy to make ahead - They store well in the fridge and freezer, so you can enjoy one whenever a pumpkin craving strikes.

How to Make Vegan Pumpkin Muffins with Cream Cheese Filling (with pictures)

Please see the recipe card at the bottom of the page for full instructions and ingredient measurements.

Begin by whisking together all of the dry muffin ingredients in a large mixing bowl. Add the wet ingredients to the bowl and mix until just combined.

Whip together the cream cheese filling ingredients using an electric hand mixer until smooth.

In a small bowl, mix together the streusel topping ingredients. Cut in the vegan butter using a pastry cutter until mixture in crumbly.

Line a cupcake pan with paper liners, skipping every other hole. Fill each liner ⅔ to ¾ of the way full.

Pipe the cream cheese filling inter the center of each muffin. Top with a generous handful of the streusel.

Bake muffins on the center rack of an oven that has been preheated to 450 degrees F (230 C) for 5 minutes. Reduce heat to 375 degrees F (190 C) and bake for an additional 10-12 minutes.

Tips & Tricks

1. Keep the cream cheese filling stable: Use cornstarch in the filling and don't over-mix to ensure it stays creamy but holds its shape when baked.
2. Measure flour correctly: Spoon the flour into your measuring cup and level it off. Too much flour can make the muffins dense.
3. Use room temperature ingredients: Make sure the vegan cream cheese is softened and the pumpkin puree is smooth. This helps the batter mix evenly.
4. Mix dry and wet ingredients separately: Combine dry spices and leavening agents in one bowl, and wet ingredients in another. Then fold them together gently to avoid over-mixing, which can make muffins tough.
5. Don't skip the streusel: The pecan streusel adds texture, sweetness, and a crunchy contrast to the soft, fluffy muffins.
6. Check for doneness carefully: Muffins are done when a toothpick inserted into the cake (avoiding the cream cheese center) comes out clean or with just a few crumbs.
7. Cool before serving: Let the muffins cool for 10-15 minutes before slicing so the cream cheese filling sets and the streusel stays intact.

Common Mistakes and How to Fix Them

Cream Cheese Filling Leaking

• Cause: Filling is too runny or overfilled.
• Fix: Add cornstarch to stabilize the filling and layer it carefully in the muffin batter. Don't overfill.

Cream Cheese Filling Dense or Rubbery

• Cause: Overmixing the filling or baking too long.
• Fix: Mix the filling just until smooth-avoid whipping it too vigorously. Bake muffins until just done, keeping an eye on the cream cheese center.

Muffins Turn Out Dense

• Cause: Overmixing the batter or packing in too much flour.
• Fix: Mix wet and dry ingredients gently until just combined. Measure flour by spooning into the cup and leveling it, don't scoop directly.

Streusel Sinking or Burning

• Cause: Topping is too heavy or oven temperature too high.
• Fix: Use cold, melted butter sparingly and sprinkle topping evenly. Bake at the recommended temperature and check early if oven runs hot.

Cream Cheese Filling Too Sweet or Bland

• Cause: Sugar ratio off or vanilla missing.
• Fix: Use light brown sugar for depth and include vanilla extract. Taste and adjust if needed before filling muffins.

Frequently Asked Questions

Best Vegan Cream Cheese Brands

When it comes to baking, using a high quality vegan cream cheese is important if you want to achieve the best results.

Here are a few of my favorite brands for baking:

1. Tofutti: Highly recommended for baking - consistently say it holds up under heat, remains smooth, and doesn't separate.
2. Violife: Excellent texture and mild flavor, which makes it versatile for desserts or frostings. It's coconut‑oil‑based and melts/bakes well in many recipes.
3. Kite Hill: Almond‑milk based and praised for its smoothness, tang, and reliability. A solid option for baking when you want a clean, dairy‑style profile.
4. Miyoko's: Cashew‑based and thick. Great for richer desserts or cheesecake‑style fillings. If you want ultra‑premium, this one fits.
5. Philadelphia Vegan Cream Cheese: The classic brand's vegan version has received praise for texture and baking performance.

What to Look For

• Baking Stability: Cream cheese that retains its structure when heated (doesn't separate) is key for fillings, frostings, and baked goods.
• Mild Tang & Flavor: A cream cheese with a subtle tang and minimal off‑notes will let your other flavors shine.
• Texture & Consistency: Smooth, thick spreads work best since they mimic dairy cream cheese in baking.
• Ingredient & Allergen Considerations: If you have nut, soy, or coconut restrictions, check the base. Some are cashew‑ or almond‑based; others use coconut oils.
• Availability & Cost: Consider what's available at your stores and whether you're willing to invest in premium brands.

Storage

. Room Temperature:

• Store in an airtight container for up to 3 days.
• Keep them away from heat or sunlight to prevent the cream cheese filling from becoming too soft.

Refrigerator:

• Place cooled muffins in an airtight container.
• They will last up to 5 days in the fridge.
• Best enjoyed slightly warmed to bring back a soft, tender texture.

Freezer:

• Freeze for up to 1 month.
• Thaw at room temperature for 15 minutes before eating.

If you make this recipe please tag @censoredbaker on Instagram!

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More vegan pumpkin recipes:

• Vegan Pumpkin Bars w/Cream Cheese Frosting
• Vegan Pumpkin Spice Latte
• Vegan Pumpkin Sugar Cookies

More vegan muffins recipes: