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Vegan Pumpkin Muffins with Cream Cheese

by Sarah McMinn / Posted: / Updated: / Disclosure: This post may contain affiliate links. Jump to Recipe Print Recipe Total Time: 35 mins

Fall into fall with these deliciously light and perfectly flavored vegan pumpkin muffins with Cream Cheese Swirl. An easy, fail-proof, autumnal pastry that will warm up your home and fill up your belly. Made in just 30 minutes!

Finished muffins stacked in a bowl

I hate to be cliché but, friends, PUMPKIN season is upon us!

My first pumpkin recipe of the year is always exciting for me. It means fall has truly arrived with all its autumnal splendor. Last year I kicked off the season with this Pumpkin and Smokey Tempeh Chili and the year before that it was my Peanut Pumpkin Curry. If you want to know my favorite pumpkin recipe from past years, I would have to say this Pumpkin Alfredo Pasta. So creamy and delicious!

But then these vegan pumpkin muffins with cream cheese came along and everything changed.

Finished recipe in a muffin tin
Table of Contents show

How to make Vegan Pumpkin Muffins {Video}

Recommended Ingredients & Equipment

These muffins are a variation of last year’s Vegan Cheesecake Muffins. Since sharing those on the blog, I have had several requests for a plain and simple vegan pumpkin muffin recipe. And so, per your request, a warm, light and fluffy, pumpkin muffin that is bursting with pumpkin flavor and fall spices.

Ingredients & Substitutions

  • All-Purpose Flour – For healthier flour options, you can use 1:1 gluten-free flour blends, buckwheat, or spelt flour.
  • Baking Soda
  • Spices – You will need cinnamon, ginger, cloves, nutmeg, and salt.
  • Pumpkin Puree – Make sure to use canned pumpkin and NOT pumpkin pie filling.
  • White & Brown Sugar – Check out my guide to vegan sugars and alternative sugar replacements. For a healthier sugar alternative, I recommend coconut sugar.
  • Applesauce – This is the binder of the recipe. You could replace it with 1/2 mashed bananas, an additional 1/2 cup of pumpkin puree, or a variety of other egg replacers.
  • Coconut Oil
  • Vanilla Extract
  • Vegan Cream Cheese

Best Vegan Cream Cheese

For the cheesecake filling, I used Go Veggie’s classic cream cheese made with coconut.

Go Veggie’s cream cheese is made from coconut for a non-GMO, no cholesterol, vegan alternative. I love Go Veggie, a company dedicated to promoting healthier lifestyles by providing delicious plant-based cheese alternatives. Their cheeses have more calcium, equal protein, less fat and fewer calories compared to dairy cheese. Their mission – to help cheese lovers enjoy all their favorite cheesy foods and feel great about it.

Recommended Equipment

For all my vegan muffin recipes, you’ll need basic kitchen equipment such as a mixing bowl, utensils, a wire cooling rack, and a muffin baking pan. I also recommend using an ice cream scoop to evenly and cleanly scoop your batter. (<<affiliate links)

Check out the full list of my recommended kitchen tools and gadgets.

How to Make Vegan Pumpkin Muffins

Step One – Make the Batter

Whisk together all your dry ingredients in a bowl. That’s your flour, baking soda, salt, and spices.

In a separate bowl (or liquid measuring cup) mix together your wet ingredients. That’s pumpkin purée, sugars, apple sauce, coconut oil, and vanilla extract.

Combine the wet ingredients with the dry, mixing until you have a uniform batter. Don’t over-mix as this will make your muffins dense and gummy.

Dry and wet ingredients for vegan muffins
Batter for Vegan Pumpkin Muffins.

Step Two – Make the Cream Cheese Swirl

In a separate bowl combine cream cheese, sugar, and vanilla extract with a fork. Stir until smooth.

Step Three – Scoop and Bake

Scoop the batter into the prepared muffin tin, filling each mold about 2/3 of the way full. Top with 1 tablespoon of cream cheese mixture and, using a toothpick, swirl to combine.

Pumpkin muffin batter in a muffin tin

Bake for 20 minutes at 350 F. To check for doneness, insert a toothpick in the middle of a muffin. The muffins are done when the toothpick comes out clean. Pull from oven and let the vegan muffins cool for 10 minutes in the muffin tin before transferring them to a wire cooling rack.

Pro Tip: Make sure to let your muffins cool in the muffin tin first. If you flip them out too quickly, the muffins may fall apart.

Stack of finished muffins on a wooden platter

Serving And Storing

Serve these muffins immediately. They come out of the oven warm, buttery, and hard to resist!

Store leftover muffins in an airtight container at room temperature for up to 5 days. You can also freeze these muffins for up to 2 months. To thaw, pull the muffins from the freezer and let them thaw at room temperature for several hours.

Tips and Tricks

  1. Make sure not to over-mix your batter. When the batter is over-mixed, it allows gluten stands to form which leads to gummy dense pastries. We’re looking for light and fluffy!
  2. Spray your muffin tin well! Or, if you’d prefer, use cupcake holders. This will prevent the batter from sticking to the pan.
  3. Fill up your muffin molds about 2/3rds of the way full. If you do much more, the muffins will spill over as they rise.
  4. Let your muffins cool for 10 minutes before flipping them out onto a wire cooling rack.

Frequently Asked Questions

Can I omit the oil?

Sure. If you would like to make this recipe oil-free, simply swap out the oil for additional applesauce at a 1:1 ratio.

Can this muffin batter be made in advance?

Yes! If you want to make this muffin batter in advance, store the batter in an airtight container in the refrigerator for up to 48 hours.

To bake the muffins, preheat the oven and bake according to the instructions. However, these muffins may take a few minutes longer to bake since the batter will be chilled. The muffins will also be slightly denser as the baking soda begins to activate once it’s mixed into the batter, causing it to be slightly less potent.

Can I make this recipe gluten-free?

For sure! For gluten-free muffins, I recommend using a 1:1 baking blend.

Stack of three Pumpkin Cream Cheese Muffins

More Vegan Pumpkin Recipes

More Vegan Muffin Recipes

Finished muffins stacked in a bowl

Vegan Pumpkin Muffins with Cream Cheese

These vegan Pumpkin Muffins with cream cheese are filled with the flavors of cinnamon and nutmeg and made extra moist with pumpkin puree.
4.88 from 8 votes
Print Pin Rate
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 18 muffins
Calories: 215kcal
Author: Sarah McMinn

Ingredients

Pumpkin Muffins

Cream Chesee Swirl

  • 8 ounce GO VEGGIE vegan cream cheese
  • 1/4 cup granulated sugar
  • 1 teaspoon vanilla extract
US Customary – Metric

Instructions

  • Preheat the oven to 350 degrees F. Spray two muffin tins with cooking oil and set aside.
  • In a small bowl whisk together flour, baking soda, spices, and salt. In a large bowl combine pumpkin puree with both sugars, mixing to combine. Add apple sauce, oil, and vanilla extract and stir until smooth. Fold dry ingredients into the wet ingredients.
  • In a separate bowl combine cream cheese, sugar, and vanilla extract with a fork. Stir until smooth.
  • Fill muffin molds 2/3 of the way full. Top with 1 tablespoon of cream cheese mixture and, using a toothpick, swirl to combine.
  • Bake for 20 minutes. Remove from oven and allow muffins to cool for 10 minutes before transferring to a wire cooling rack to cool completely.

Notes

Serving and Storing – Serve these muffins immediately. They come out of the oven warm, buttery, and hard to resist! Store leftover muffins in an airtight container at room temperature for up to 5 days. You can also freeze these muffins for up to 2 months. To thaw, pull the muffins from the freezer and let them thaw at room temperature for several hours.
Make in Advance – If you want to make this muffin batter in advance, store the batter in an airtight container in the refrigerator for up to 48 hours. To bake the muffins, preheat the oven and bake according to the instructions. However, these muffins may take a few minutes longer to bake since the batter will be chilled. The muffins will also be slightly denser as the baking soda begins to activate once it’s mixed into the batter, causing it to be slightly less potent.
Recipe Tips
  1. Make sure not to over-mix your batter. When the batter is over-mixed, it allows gluten stands to form which leads to gummy dense pastries. We’re looking for light and fluffy!
  2. Spray your muffin tin well! Or, if you’d prefer, use cupcake holders. This will prevent the batter from sticking to the pan.
  3. Fill up your muffin molds about 2/3rds of the way full. If you do much more, the muffins will spill over as they rise.
  4. Let your muffins cool for 10 minutes before flipping them out onto a wire cooling rack.

Nutrition

Calories: 215kcal | Carbohydrates: 31g | Protein: 2g | Fat: 9g | Saturated Fat: 6g | Sodium: 206mg | Potassium: 26mg | Fiber: 1g | Sugar: 20g | Vitamin A: 10IU | Vitamin C: 0.1mg | Calcium: 17mg | Iron: 0.8mg
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Reader Interactions

Hi, I’m Sarah. I’m a 14-year (and counting) vegan, professionally trained photographer, former pastry chef, founder of My Darling Vegan, and author of the 4-Week Vegan Meal Plan.

Follow me on Instagram, Facebook, and Pinterest and read more about me here.

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Comments

  1. Natalia says

    5 stars
    Just made these, did mini muffins instead of regular sized and they turned out fantastic! Just baked for about 5 minutes less than what was recommended for the regular muffins. Toffuti brand cream cheese is also a great option and worked perfect for these. Thanks for my new favorite fall recipe !

    Reply

  2. Linda says

    I wanted to love these. Seems recipe may call for too much oil? And then the 1 tsp of cheese swirled in made mine a gooey blob :-(. Will see if cooling helps. But right now they are just flat and wet.

    Reply

  3. Christine says

    4 stars
    I made these using the Miyokos brand dairy-free cream cheese and they turned out great! I don’t think I overmixed the batter but they did turn out more dense than fluffy, and very moist. They’re good warmed up in the microwave for breakfast. Thanks for the recipe!

    Reply

  4. Liz says

    I did see the answer I was looking for in the comments but you might to add the can size (15oz) for the pumpkin puree. Excited to try these!

    Reply

    • Sarah says

      It’s a sweet muffin. If you half the sugar it won’t only affect the taste but the texture significantly. If you give it a try, let us know how it works for you.

      Reply

  11. Linda from Veganosity says

    September has been cool in Chicago this year, although our Indian summer is going to hit us this weekend, just in time for our 20 miler training run. Sweating is about to get real again. I’d love to stuff my face with these muffins after our run on Sunday. I think I need to make a big batch!

    Reply

  16. Shari Wexler says

    These look amazing and appropriate for my beginner self! The photo shows them in cupcake holders but the recipe says to spray the muffin tins with cooking oil. Does that need to be done if you’re using cupcake holders?

    Reply

  17. Jenn says

    You should come visit me. The temps have been mostly in the 60’s to low 70’s. The smell of autumn is in the air, apple festivals are in full force, and even the leaves are starting to turn. I’m in heaven! The only thing that would make it better is if I was wrapped in a blanket in front of a bonfire on a chilly evening shoving these delicious muffins in my face two at a time!

    Reply
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