These chocolate chip vegan pumpkin muffins are moist, fluffy, and perfectly sweet. They are vegan, and super easy to make too! Perfect for breakfast, dessert, or a midday snack.

Just the perfect chili weather for these vegan pumpkin Muffins.

There’s a chill in the air which means it’s time for pumpkin everything!

I’ve been working a lot with pumpkin lately and I just can’t get enough.

A plate of one bowl easy pumpkin muffins with low sugar chocolate chips on top.

These vegan chocolate chip pumpkin muffins are perfect for an on-the-go breakfast or snack this season.

Additionally, they can be dressed up for a dessert option as well.

What Makes these Whole Wheat Vegan Pumpkin muffins Different?

A stack of three healthy pumpkin chocolate chip muffins. There is a bite in the muffin on top.

Refined sugar-free, oil free, nut free, and vegan

These chocolate chip pumpkin muffins are sweetened using only coconut sugar.

It is naturally vegan-friendly as well.

Can be made Gluten-Free

If you are looking to make this recipe gluten-free, you can substitute the whole wheat flour with a 1:1 ratio of gluten-free flour instead.

Ingredients Needed for Pumpkin Chocolate Chip Muffins

A pan of vegan pumpkin chocolate chip muffins batter ready to be baked.

Pumpkin puree

Not to be confused with pumpkin pie filling.

Pumpkin puree should only contain pumpkin/squash on the ingredient label.

No other added sugar or spices should be on the label.

You can also make homemade pumpkin puree using my recipe in this post.

Apple cider vinegar

It helps baked goods to rise.

Milk of choice

Some of my favorites include oat milk (nut-free), coconut milk (not canned), and almond or cashew milk.

Whole wheat flour

Coconut sugar

Less processed than white sugar, it is unrefined.

Pumpkin spice

It consists of spices including cinnamon, nutmeg, ginger, cloves and sometimes all spice.

How to Make Pumpkin Chocolate Chip Muffins

Directions how to make whole wheat pumpkin muffin in a bowl.

I made these chocolate chip pumpkin muffins very similar to the way I made these sweet potato muffins, minus the sweet potato of course.

First, combine the pumpkin puree, apple cider vinegar and milk. Set aside.

Then, in a separate bowl, mix whole wheat flour, coconut sugar, and pumpkin spice.

Gradually add wet ingredients to dry and thoroughly combine.

Next, Fold in chocolate chips.

Scoop the muffin batter into the muffin tin, filling almost to the top.

Sprinkle more chocolate chips (optional) across the top of muffins and bake for 20-25 minutes until a toothpick can be inserted in the center and comes out clean, or until the internal temperature reaches 200 F.

Optional toppings to spice up your Vegan pumpkin muffins:

Freshly baked vegan whole wheat pumpkin muffins with chocolate chips on top are placed on a cooling rack.

Besides chocolate chips, you can also add other mix-ins and toppings to spice up these pumpkin muffins.

Some of my favorites:

  • Pecans (for non-nut-free version)
  • Raisins
  • Coconut sugar + cinnamon

How to Serve Vegan Pumpkin Chocolate Chip Muffins

A piece of fluffy vegan pumpkin muffins with chocolate chips served with peanut butter. There is a bite.

I love to throw a dollop of plant-based or full-fat yogurt on top of these muffins for a little protein boost.

Additionally, it adds a creamy texture that pairs well with the density of the muffin. 

Last but not least, warming the muffins up a bit and then adding butter or ghee makes a great breakfast to go along with your morning coffee!


Tom has already requested me making these Pumpkin muffins more often.

How to Store Whole Wheat Pumpkin Muffins

A plate of vegan whole wheat pumpkin muffins. The middle one has a bite in it. The most Moist and fluffy pumpkin muffin this fall.

The best way to store these delicious pumpkin muffins is in an air-tight container for up to 5 days.

However, they can be frozen if you need them to last longer or you want to make a larger batch for meal prepping.

To reheat, let it thaw in room temperature for a few hours.

You can also microwave it 20 – 30 seconds at a time. Add more time if needed to make sure not to over-heat them.

Tips for Best Vegan Pumpkin Muffins

A plate of vegan whole wheat muffins. The middle one has a bite in it. The most Moist and fluffy pumpkin muffin this fall.

Here are a few tips and tricks to take your chocolate chip pumpkin muffin up a notch.

Sift dry ingredients.

Sifting dry ingredients helps to get rid of any clumps and ensure thorough mixing of ingredients.

Mix by hand.

Mixing by hand can help to prevent over mixing which can lead to a rubbery muffin. Nobody wants that!

Use a variety of toppings.

Switch up your muffins and keep a variety on hand by adding different toppings to the muffins before baking.

What’s your favorite kind of pumpkin muffin? Leave a comment below!


A piece of fluffy vegan pumpkin muffins with chocolate chips served with peanut butter. There is a bite.


A plate of vegan whole wheat pumpkin muffins. The middle one has a bite in it. The most Moist and fluffy pumpkin muffin this fall.

Get the recipe:Vegan Pumpkin Chocolate Chip Muffins

These easy vegan pumpkins muffins with chocolate chip vegan are delicious. They are nut-free, oil-free, and have no refined sugar.
4.38 stars (8 reviews)


  • 1 cup pumpkin puree
  • 2/3 cup milk of choice
  • 1 tbsp apple cider vinegar
  • 3/4 cup whole wheat flour, packed
  • 1/3 cup brown sugar
  • 1 tsp pumpkin spice
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 1/2 cup chocolate chips


  • Preheat the oven to 350 F.
  • In a mixing bowl, blend together all the wet ingredients with a hand mixier -pumpkin puree, milk, and apple cider vinegar.
  • In a large bowl, mix together all the dry ingredients (except for chocolate chips) – whole wheat flour, brown sugar, baking soda, powder, and pumpkin spice
  • Pour the wet ingredients mixture in the dry ingredients. Gently combine with a spatula. Fold in 2/3 of the chocoalte chips. Save the rest to add on top.
  • Line and grease a muffin pan. Use a medium cookie dough scooper to fill up each muffin cups close to the top.
  • Sprinkle the rest of the chocolate chips on top.
  • Bake 20 – 23 minutes or until a toothpick comes out clean after inserting in the middle of the muffin. If using a food thermometer, the internal temperature should reach around 200F.
  • Let it cool for 10 minutes on a cooling rack. Enjoy!
Serving: 1g, Calories: 126kcal, Carbohydrates: 21g, Protein: 3g, Fat: 4g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Cholesterol: 1mg, Sodium: 208mg, Fiber: 2g, Sugar: 11g

The Nutrition Facts above are specific to the ingredients I chose to use for this recipe, which may vary.

A plate of one bowl easy vegan pumpkin muffins with low sugar chocolate chips on top.