These lightly sweet, whole grain, vegan pumpkin muffins have been a snack staple for us since pumpkins came into season in September. It’s a nice replacement for banana, using a local ingredient that works in much the same way.
Like most of the muffin recipes on OE, whole grain spelt flour forms the base here for a higher fibre snack or breakfast. You can use other flour (see below). There are a couple things to note about pumpkin puree so please read through before baking.
For a similar GF option, try my gluten-free pumpkin muffins, also with chocolate. These are adapted from my banana blueberry muffins.
Why You Should Try This Recipe
With more protein and fibre than other muffins due to whole grain flour and the addition of pumpkin, these are an energy-packed snack that feel like a treat thanks to the added dark chocolate.
- It’s a one-bowl recipe: everything is mixed in the same bowl – less dishes for you!
- Pumpkin is a great alternative to banana: while I love banana muffins as much as anyone, it’s nice to use a local alternative.
- They taste like autumn: with the subtle pumpkin and warm spices, this is the season in a muffin. They’re just as good right through winter, too.
Ingredients

Ingredient Notes and Substitutions
- Spelt flour: this is whole grain spelt flour. You can use regular whole wheat flour, another low-gluten flour like einkorn, or even plain all-purpose.
- Pumpkin: this should be plain puree with no other ingredients added to it. Sugar pie and butternut squash make perfect puree for this recipe, but Hokkaido is a bit dry.
- Spices: cinnamon and nutmeg are listed, but you could also use cardamom, cloves, or a spice mix you like.
- Dark chocolate chips: make sure to check that the chips are vegan if necessary. You could sub cocoa nibs if preferred.
- Milk: I always use oat milk, but any kind of milk can be used (except canned coconut milk, it’s too thick). You can sub water in a pinch.
Step by Step
1. Mix the wet ingredients: whisk the pumpkin, milk, oil, and vanilla together.
2. Add dry ingredients: add the remaining ingredients and mix, then fold in the chocolate chips.

3. Spoon into muffin cups: try to make them as even as possible.
4. Bake: for about 20 minutes, or until golden.
If you can’t see the recipe video, please watch it here on YouTube instead.
Recipe Notes
Not all pumpkins are equal and the recipe will have to be adapted slightly based on the pumpkin used to make puree. Some bake up really dry and will make for dry muffins. If yours is more hard than liquid, I recommend mixing some water in. It should be slightly thicker than applesauce in consistency for best results.
While I’m sure you can use canned pumpkin puree, I can’t get it here, and haven’t tested these using it. Don’t use pumpkin pie filling.
How to Store
Storage: these will keep for 2-3 days in a sealed container at room temperature, but should be refrigerated for any longer storage.
Freezing: place cooled muffins in an airtight container an freeze for up to six months.

Expert Tips
- Don’t over mix: with any spelt recipe, you want to be careful to avoid over-mixing so you don’t end up with tough muffins. Mix until just combined.
- Use mini chips: if you can get them, mini chocolate chips are perfect for this recipe. You can use chopped chocolate if preferred.
- Choose a tasty pumpkin: halloween pumpkins are not meant to be roasted up and eaten – choose a variety that you’d roast up and eat.
More Whole Grain Muffin Recipes
Raspberry Yogurt Muffins
Chocolate Beet Muffins
Vegan Banana Chocolate Muffins
Chocolate Raspberry Muffins
If you make these Pumpkin Chocolate Chip Muffins or any other muffin recipes on Occasionally Eggs, please take a moment to rate the recipe and leave a comment below. It’s such a help to others who want to try the recipe. For more OE, follow along on Instagram, Facebook, and Pinterest, purchase the Occasionally Eggs cookbook, or subscribe for new posts via email.
Chocolate Chip Pumpkin Muffins
Ingredients
- 300 grams pumpkin puree
- 120 ml oat milk
- 50 ml olive oil
- 1 teaspoon vanilla extract
- 260 grams whole grain spelt flour
- 80 grams coconut sugar
- 2 teaspoons cinnamon
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon nutmeg fresh ground is best
- ¼ teaspoon sea salt
- 100 grams dark chocolate chips
Instructions
- Preheat the oven to 180°C (350°F) and grease or line a 12-cup muffin tin.
- Add the pumpkin puree, milk, olive oil, and vanilla to a large mixing bowl. Whisk well to combine.300 grams pumpkin puree, 120 ml oat milk, 50 ml olive oil, 1 teaspoon vanilla extract
- Add the flour, coconut sugar, cinnamon, baking powder, baking soda, nutmeg, and salt to the bowl. Use a wooden spoon or spatula to mix until just combined, being careful not to over mix.260 grams whole grain spelt flour, 2 teaspoons cinnamon, 2 teaspoons baking powder, 1/2 teaspoon baking soda, 1/2 teaspoon nutmeg, 1/4 teaspoon sea salt, 80 grams coconut sugar
- Add the chocolate chips to the batter and gently fold in to incorporate.100 grams dark chocolate chips
- Spoon the muffin batter in to the prepared muffin tin, trying to make equally-sized muffins. Bake for 20-22 minutes, or until lightly golden and the muffins pass the skewer test.
- Cool the muffins in the tin for about five minutes before carefully removing and cooling fully on a wire rack. Store in a sealed container for 2-3 days or freeze for up to three months.
Video
* For American cup measurements, please click the pink link text above the ingredient list that says ‘American’.
Nutrition
Nutrition is provided as a courtesy and is an estimate. If this information is important to you, please have it verified independently.
Dana says
I loved these muffins! I used Hokkaido and it worked very well after mixing some more milk to the batter.
Thank you for another great recipe!