Make these Healthy Pumpkin Chocolate Chip Muffins for the perfect fall treat. These healthy pumpkin muffins are made extra sweet with a few chocolate chips.

Quick
Minimal prep
You’ll Learn: How to batch, store, and reheat for meal prep
Worth It: Packs plenty of flavor and gentle sweetness for a cozy snack or breakfast
Bonus: Easy to tailor to common diets

Healthy pumpkin muffins are even better when you add chocolate chips
When I was a freshman in college I had a super long walk from one part of the campus to another. On Fridays I would treat myself to a massive pumpkin chocolate chip muffin and savor it as I walked.
Now whenever I have a pumpkin spice muffin I remember that time in my life. I found a can of pumpkin in my pantry last week and even though its not the fall, I went to town making a bunch of pumpkin recipes.
These healthy pumpkin chocolate chip muffins are the only sweet recipe that I came up with. These muffins are a slightly sweet and spiced snack or breakfast that are perfect with a cup of coffee.
How to serve
I like to serve these healthy pumpkin muffins as a quick and easy breakfast. Slather them with some creamy peanut butter or almond butter for an extra boost of protein.
They are also perfect as an afternoon pick me up with a cup of coffee. I like to make a pumpkin cream cold brew with this homemade pumpkin spice syrup.
Serve these chocolate chip pumpkin muffins alongside the cookies and pies at thanksgiving dinner. They are perfect for little kids to grab and go.

What kitchen tools will I need to make these almond flour pumpkin muffins?
- Muffin tin
- Muffin tin liners, parchment paper or cooking spray
- Mixing bowls
- Measuring spoons
- Measuring cups
- Liquid measuring cup
- Spatula
- 1.5 tbsp measuring scoop
If you run out of paper muffin tin liners, you can easily make your own with parchment paper. Cut parchment into 5″x5″ squares.
Then, press them down into muffin tins and crease the edges. The healthy pumpkin muffin batter will weigh down the paper and create a little cup.
tip for perfect healthy pumpkin muffins
If you want perfectly formed muffins, spray the inside of the muffin cups or muffin liners with cooking spray before you pour the batter into them. Then, when they are finished, the muffin comes out clean.

What ingredients will I need to make these pumpkin chocolate chip muffins?
You will be amazed how easy it is to make these gluten free pumpkin spice muffins with just a few basic ingredients. I recommend using the mixture of almond flour and coconut flour for the best grain free muffin texture.
- Eggs
- Pumpkin puree
- Maple syrup
- Coconut oil
- Almond flour
- Coconut flour
- Baking soda
- Baking powder
- Salt
- Pumpkin pie spice
- Chocolate chips
Is canned pumpkin and pumpkin puree the same thing?
Yes! Canned pumpkin and pumpkin puree are usually the same thing. Check the can and make sure that the only ingredient is pumpkin.
You do not want to use canned pumpkin pie filling for this recipe because it is canned pumpkin mixed with other ingredients.
Make them dairy free
It is super easy to make these healthy pumpkin muffins dairy free. Just replace the semi sweet chocolate chips with dairy free chocolate chips.
You can also leave the chocolate chips out completely and replace them with raisins or dried cranberries. If you like a crunch in your muffins, mix some walnut pieces into the batter.

Let’s make Healthy Pumpkin Chocolate Chip Muffins!
Step 1: Mix wet ingredients
First, preheat oven to 350F and line muffin tin with liners. Then, add eggs, maple syrup, coconut oil, and pumpkin puree to a large mixing bowl. Mix thoroughly.
Step 2: Fold in dry ingredients and chocolate chips
Next, add almond flour, coconut flour, baking powder, baking soda, pumpkin pie spice, and salt to a separate mixing bowl and mix thoroughly. Fold fry ingredients into wet and mix with a spatula. Then, fold the chocolate chips into the batter.
Step 3: Bake and cool muffins
Next, scoop 3 tbsp of batter into each of 10 muffin tins. Place in the oven and bake at 350F for 30 minutes. Finally, remove from the oven and cool on baking rack.

How should I store these pumpkin chocolate chip muffins?
Allow these healthy pumpkin muffins to cool completely. Then, store on the countertop for a couple of days in an airtight container.
Store them in the fridge for up to one week. Reheat them in the toaster oven or on the stove top sliced in half.
You can freeze these muffins for up to three months. Defrost them individually in the fridge before reheating them.
Check out these other healthy muffin recipes!
You can find the full recipe below. If you make this recipe, please rate and review it in the comments, or share it with me on Instagram!

You can find the full recipe below. If you make this recipe, please rate and review it in the comments, or share it with me on Instagram!
Email Recipe for Later

Recipe
Healthy Pumpkin Chocolate Chip Muffins
Ingredients
- 3 eggs
- 1/2 cup pumpkin puree
- 1/2 cup maple syrup
- 1/4 cup melted coconut
- 1 1/2 cups almond flour
- 2 tbsp coconut flour
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp salt
- 2 tsp pumpkin pie spice
- 1/2 cup chocolate chips
Instructions
- Preheat oven to 350F and line 10 muffin cups in a muffin tin with liners – if you don’t have liners you can use squares of parchment paper
- Add eggs, pumpkin puree, maple syrup, and melted and cooled coconut oil to a large mixing bowl and mix together thoroughly
- In a separate mixing bowl combine almond flour, coconut flour, baking powder, baking soda, salt, and pumpkin pie spice
- Fold dry ingredients into wet with a spatula
- Then fold in chocolate chips
- Take 3 tbsp of batter and place in each of 10 muffin tin slots
- Place muffin tin in the oven and bake for 30 minutes
- Remove from the oven and allow to cool slightly in the muffin tin before transferring to a cooling rack to cool fully
Nutrition Information
This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition data is gathered primarily from the USDA Food Composition Database, whenever available, or otherwise other online calculators.

















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