These easy healthy pumpkin chocolate chip muffins turn out moist and fluffy and so yummy! Mix up a batch for breakfast and snacks or freeze some for later…if you have any left!

Here’s one thing I’ve learned over the years while cooking real food for my family: Anytime you make something that the kids eat without complaining AND they eat the whole dish, make it over and over again until they ask you to stop.
And then freeze whatever they couldn’t finish and serve it again in a month!
That’s what usually happens when I make things like Double Chocolate Waffles and Pumpkin Donuts and Sourdough Pancakes.
And that’s exactly what happened when I made these pumpkin chocolate chip muffins!
WHY MAKE PUMPKIN CHOCOLATE CHIP MUFFINS
There are A LOT of recipes for pumpkin chocolate chip muffins out there, but this is my favorite fall treat!
Here’s why we love this particular recipe so much:
- Freezer-friendly. Bake extras now and freeze them for quick breakfasts later. Or, if you’re short on time, use my trick for freezing muffin batter!
- A whole can of pumpkin! How often can you say that a MUFFIN contains this amount of vegetables?!
- Quick and easy. Don’t let the long list of ingredients fool you – these muffins come together really fast.
- Whole grains! Unlike a lot of muffins, these actually taste BETTER when you use whole-grain flour. (I mill my own einkorn with a MockMill grain mill. You can read my honest review here.)
- Basic ingredients. If you have pumpkin purée on hand, I bet you already have everything else too!
- One bowl. You don’t HAVE to have a mixer to make these. You could easily get it done with just one large mixing bowl! (Although if you have one, muffins are just one of my 40+ creative ways to use a stand mixer!)
On top of all of that, this pumpkin muffin recipe isn’t finicky. You don’t have to baby the batter or take any special care when mixing it up.
It’s as simple as stir wet + add dry + fold chips + bake. And that’s it!

INGREDIENTS FOR PUMPKIN CHOCOLATE CHUNK MUFFINS
Here’s what you need to make these amazing pumpkin chocolate chunk muffins:
- Whole Wheat Flour. Whole grain einkorn works too. If you only have all purpose flour on hand, use it!
- Granulated Sugar. I use Turbinado.
- Baking Soda and Baking Powder. To give the muffins lift and make them fluffy.
- Salt. Not all salts are made the same! I love Ava Jane’s Kitchen because it doesn’t have microplastics (gross, right?) and it’s SO GOOD! Plus, you can get a free 8oz. bag of sea salt (just pay shipping and handling!).
- Cinnamon + Ginger + Nutmeg + Cloves. The standard flavors to go with pumpkin! You could substitute Homemade Pumpkin Spice instead, but I like how these muffins call for a bit of extra cinnamon.
- Eggs. Used for binding and lifting, eggs also add richness to the muffins.
- Pumpkin Puree. Use pureed pumpkin here, not pumpkin pie filling. If you have baking pumpkins around, you can make your own puree.
- Coconut Oil. Pumpkin and oil together give the finished muffins a soft, moist texture. Melted butter would also work, or you can replace some of the coconut oil with applesauce.
- Chocolate Chips. I use 70% dark chocolate chips. Semisweet chocolate chips or chocolate chunks work too. Or if you want extra chocolate chips, use mini chocolate chips!

HOW TO MAKE PUMPKIN AND CHOCOLATE CHIP MUFFINS
I mentioned that you can make this pumpkin and chocolate chip muffin recipe in one big bowl if you choose not to use a stand mixer. The instructions are simple and straightforward in either case.
Step 1. Preheat the oven to 400F.
Step 2. In a large bowl or the bowl of a stand mixer, add the eggs, pumpkin puree, and coconut oil, and mix to combine.
Step 3. Add the dry ingredients – whole wheat flour, granulated sugar, baking soda, baking powder, salt, cinnamon, ginger, nutmeg, and cloves – and stir until combined.
Step 4. Fold in the chocolate chips.
Step 5. Line two muffin tins with silicone muffin liners and use a large cookie scoop to scoop the batter into the muffin cups, filling them ⅔ of the way full.
Step 6. Bake for 20 minutes, or until the tops are golden brown and a toothpick inserted into the center of a muffin comes out clean. Let cool on a wire rack.

PUMPKIN AND CHOCOLATE MUFFINS TIPS
Whether you use a stand mixer or a bowl, I HIGHLY recommend investing in a large cookie scoop. I have this one, and it makes pouring muffin batter CRAZY fast and easy. Plus, as a bonus, every muffin is the same size… so neither of the kids comes to me early in the morning whining “But THEY have a bigger muffin!”
I also recommend using silicone muffin liners. They’re reusable, and once you make the initial investment, they’ll last you forever! Plus, you’ll never run out, as you do with paper liners. That means you can make pumpkin and chocolate muffins whenever a craving hits!
Store any extra pumpkin and chocolate chip muffins in an airtight container at room temperature for up to 3 days or freeze for up to 3 months.
You can also add chopped nuts to the pumpkin muffins. Pecans or walnuts would be a yummy addition!

PUMPKIN MUFFINS CHOCOLATE CHIPS FAQS
Should you use canned pumpkin? Or fresh pumpkin?
You can you either one. I think canned pumpkin puree has more of a “pumpkin” flavor, so that’s what I use. But fresh pumpkin will work! (If you’ve never made it before, here’s how to make homemade pumpkin puree.)
Are these pumpkin chocolate chip muffins healthy?
We’re using whole grains and healthy fat, so I say yes! Guilt-free treats!
You can make them a smidgen healthier by using dark chocolate chips. You can also use 50/50 honey and maple syrup, instead of the granulated sugar. I personally haven’t tested that in THIS recipe, but I’ve done that MANY times in other muffin recipes and they’ve always turned out delicious.
Can you make pumpkin muffins chocolate chips gluten-free?
I haven’t tested this, but if you have a gluten free flour blend that you use often and successfully in baking recipes, then it should work here too! Dairy-free chocolate chips would work too if you need to make this allergy friendly!

MORE TASTY MUFFIN RECIPES
- 5-Ingredient Banana Bread Muffins
- Peanut Butter Chocolate Chip Muffins
- Banana Nut Muffins with Crumb Topping
- Zucchini Muffins with Apples and Carrots
- Banana Chocolate Chip Muffins
- Applesauce Muffins

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Pumpkin Chocolate Chip Muffins
These easy healthy pumpkin chocolate chip muffins turn out moist and fluffy and so yummy! Mix up a batch for breakfast and snacks or freeze some for later…if you have any left!
- Prep Time: 5 minutes
- Cook Time: 20 minutes
- Total Time: 25 minutes
- Yield: 21–23 muffins. 1x
- Category: Dessert
- Method: Bake
- Cuisine: American
Ingredients
Dry Ingredients
- 3 cups whole wheat flour
- 1 cup granulated sugar (I use Turbinado)
- 1 tsp baking soda
- 2 tsp baking powder
- 1 tsp salt
- 2 tsp ground cinnamon
- ½ tsp ground ginger
- ½ tsp ground nutmeg
- ¼ tsp ground cloves
Wet Ingredients
- 4 eggs
- 1 (15oz) can pumpkin puree (not pumpkin pie filling)
- 1 cup melted coconut oil
Chocolate Chips
- 1 cup chocolate chips
Instructions
- Preheat the oven to 400F.
If you’re using a mixing bowl: - Combine all the dry ingredients.
- Add the wet ingredients and stir until combined.
- Proceed with step #7.
If you’re using a stand mixer: - Mix all the wet ingredients together.
- Add the dry ingredients, except the chocolate chips.
- Fold in the chocolate chips.
- Line two muffin tins with silicone muffin liners and using a large cookie scoop, scoop the batter into the muffin cups.
- Bake for 20 minutes, or until the tops are golden brown.
Notes
- Whether you use a stand mixer or a bowl, I HIGHLY recommend investing in a large cookie scoop. I have this one, and it makes pouring muffin batter CRAZY fast and easy. Plus, as a bonus, every muffin is the same size… so neither of the kids comes to me early in the morning whining “But THEY have a bigger muffin!”
- I also recommend using silicone muffin liners. They’re reusable, and once you make the initial investment, they’ll last you forever! Plus, you’ll never run out, as you do with paper liners. That means you can make pumpkin and chocolate muffins whenever a craving hits!
- Store any extra pumpkin and chocolate chip muffins in an airtight container at room temperature for up to 3 days or freeze for up to 3 months.
- You can also add chopped nuts to the pumpkin muffins. Pecans or walnuts would be a yummy addition!
Nutrition
- Serving Size: 1 muffin
- Calories: 251
We have a coconut allergy in the house. I am going to substitute vegetable oil and report back. I will also be using GF flour.
Hi Susan!
Let us know how they come out! 🙂
Could these be made with less oil? I have to eat lowfat and the whole cup of oil would be way too much for me.
Hi Yvonne,
Plain unsweetened applesauce is always a good replacement for oil in muffins. I haven’t tried it in this recipe myself, but I’m sure it would be tasty. Let us know if you try it. 🙂
Sounds Delicious! I love pumpkin muffins, and yes I have tried several versions. I can’t wait to try yours! And thanks for the tip about the large cookie scoop – I love anything that makes tasks faster!
You’re very welcome Adrianne! I hope you like these as much as we do!