Indulgent Whole Wheat Pumpkin Chocolate Muffins studded with chocolate chips. Moistened with just pumpkin puree and sweetened with sugar-free maple syrup, these healthy chocolate pumpkin muffins are the ultimate oil free and low calorie fall breakfast or dessert!

I know we’re way past Thanksgiving and all the fall recipes at this point, but I’m sure a lot of us still have a bunch of canned pumpkin lying around.

Well this chocolate flavored pumpkin recipe is a great way to use it up.

Why?

These muffins are:

Healthy
Have no oil and no sugar
Use Whole Wheat Flour
Work for Breakfast or Dessert

And the best one:

All you taste is CHOCOLATEY GOODNESS!

Ingredients for Whole Wheat Chocolate Pumpkin Muffins

If you thought whole wheat was all you’re getting in these chocolatey pumpkin muffins, well they also have no oil, no sugar and no buttermilk either!

Here’s all the ingredients

Whole Wheat Pastry Flour for the light and fluffy texture you get from all purpose, but with whole grains
Cacao Powder or Unsweetened Cocoa Powder so there’s no added sugar in here
Pumpkin Puree like the one from Libbys; Make sure it’s not pumpkin pie filling (this has sugar and such added)
Sugar free Maple Syrup that’s sweetened with Monk fruit or Stevia
Almond Milk to add moisture to the muffins, but keep them dairy free.
You can use normal milk if non dairy isn’t a restriction
Eggs
Pumpkin Pie Spice or make your own with a blend of cinnamon, nutmeg, cloves and ginger; There’s plenty of recipes online.
Baking Soda and Baking Powder – you need them both for that perfect rise!

And then for a double chocolate pumpkin muffin – and some aesthetic too – sugar-free, stevia sweetened Chocolate Chips.
I use the ones from Lily’s.

How to make Healthy Chocolate Pumpkin Muffins

These healthy pumpkin muffins are super easy to make, and take less than 30 minutes from start to end!

Preheat your oven to 350°F and line 14 cups of a muffin tin with cupcake lines. You need a 12 cup pan and 2 more cups.
Lightly spray the insides with oil spray (so the muffins come off easily.

In a large bowl, whisk the dry ingredients: whole wheat pastry flour, cacao or cocoa powder, pumpkin pie spice, baking soda and baking powder.
Set aside.

In a large bowl whisk the wet ingredients: pumpkin puree, maple syrup, almond milk and eggs.

Add the dry mix to the wet and gently fold together using a large spoon or spatula. DO NOT OVER-MIX the batter or too much gluten will form from the whole wheat flour and make the pumpkin muffins dense at the bottom.

Divide the mix among the muffin cups, filling them about ¾ way to the top.
Optionally, top with Chocolate Chips

Bake the muffins for about 20 minutes until a tester inserted into the center comes out dry.

To make a whole wheat chocolate pumpkin bread, use a parchment lined loaf pan and bake for about 50-55 minutes. A tester or toothpick should come out dry again.

How to Store Pumpkin Muffins

You can store homemade pumpkin muffins on the countertop, fridge or freezer for a meal prep breakfast or dessert.

Wrap the muffins in plastic wrap or place them in an airtight container and you can keep them on the countertop for 2-3 days, fridge for 5 days or freezer for 2-3 months.

Now you can have pumpkin spice chocolate muffins much after Thanksgiving too!

How to defrost frozen muffins:

Do not use the microwave to defrost these frozen pumpkin muffins – you want to let them thaw and come to room temperature naturally.

Just leave them out on the countertop, or place them in the fridge the previous night.

Tips for Perfect Whole Wheat Pumpkin Muffins

Use Pumpkin Puree and not pumpkin pie filling. This can either be canned or homemade.

Add dry mix to wet and fold. Don’t over-mix the batter or the gluten from the whole wheat flour will give you dense pumpkin chocolate muffins instead of moist.

Spray the cupcake liners with cooking spray – this will allow the muffins to come off easily, and you won’t lose precious muffin!

Alternatives for Double Chocolate Pumpkin Muffins

If you don’t have whole wheat pastry flour, make blend of whole wheat flour and all purpose flour. Use a 1:1 ratio here.

To replace almond milk, you can use any other milk.

Honey in place of maple syrup is another option, but these chocolate muffins won’t be sugar free anymore.

You can also make double chocolate chip pumpkin muffins by folding in more chocolate chips into the batter.

More Healthy Whole Wheat Pumpkin Recipes to Try