These bite-sized pumpkin chocolate chip muffins are the perfect afternoon snack or make-ahead breakfast. Plus, they’re full of healthy ingredients, so you can feel totally justified in having seconds…or more!

Tis the season for pumpkin and chocolate chip recipes. It’s just one of those combinations that works perfectly together. You can use them in bread, cookies…or these delicious mini muffins!
Muffins are a staple around our house. They are one of my kids’ favorite snacks. I make big batches, freeze them, and then just warm them up in the microwave quickly when the hungry monsters start circling around me. We love these banana chocolate chip muffins and these healthy blueberry muffins…and this time of year, we’re all about the pumpkin muffins.
There are plenty of recipes for pumpkin muffins out there, but since we eat these most often as a snack rather than dessert, I wanted a healthier version that wasn’t packed with sugar and butter.
I’ve been developing this recipe over the past year, and I’ve finally got it just the way I like it.
These muffins use whole wheat flour, maple syrup instead of refined white sugar, and they just use enough coconut oil to make them tender without being greasy.
The real beauty of this recipe though is that it is incredible adaptable!
Options for modifying this recipe:
Flour: The basic recipe calls for using whole wheat flour. Whole wheat is super healthy and hearty; it’s high in fiber and other important nutrients (like B vitamins). If you’re not used to whole wheat, you can also use half wheat and half white flour…or look for whole white wheat flour. Last time I made these, I even tried out using oat flour (just blend up oatmeal until you get a normal flour-like texture) and it was delicious!
Sugar: This recipe calls for using maple syrup instead of granulated white sugar. I love the depth of flavor the maple gives these muffins, and maple syrup is filled with beneficial minerals and antioxidants. Just make sure you’re using real maple syrup, not cheap maple-flavored corn syrup. You can also substitute honey. If you’re out of both of those, you can still use normal sugar.
Oil/Butter: For this recipe, I used coconut oil. Keep in mind that coconut oil is solid at a cool room temperature, so if all your liquid ingredients are refrigerator cold, the coconut oil will solidify when it hits the batter and make it lumpy. To prevent this, warm up the milk and syrup before combining them with the melted coconut oil. Don’t microwave the eggs though! If you don’t have coconut oil, you can still use regular vegetable oil or melted butter instead.
Spices: The recipe calls for 2 teaspoons of pumpkin spice blend, but you can easily make your own. In fact, I have never purchased pumpkin spice blend. Here’s my recipe for a quick DIY pumpkin spice blend:
- 1 teaspoon ground cinnamon
- ½ teaspoon ground ginger
- ¼ teaspoon ground nutmeg
- ¼ teaspoon ground allspice or cloves
Tada! You have pumpkin spice!
See? The options are endless. You can sub ingredients in and out to use whatever you have on hand in your kitchen. Go ahead and make them right now!

Answers to your burning questions:
(or something like that…)
Can I freeze these muffins?
Yes! I often double my muffin recipes and freeze the extras. Just place them in an airtight zip top bag an pop them in the freezer for up to a month (or more…you just risk freezer burn if they get lost in the back for too long).
Can I make this recipe into normal sized muffins?
Absolutely. Often, I’ll double the recipe and fill up my mini muffin pan with one batch. Then I use the rest of the batter to make regular sized muffins. The recipe works exactly the same for mini muffins or regular sized; just adjust the cooking time (12-14 minutes for minis, 18-22 minutes for regular).
Let’s get to the recipe, shall we?
Enjoy!

Mini Pumpkin Chocolate Chip Muffins
Ingredients
- 1 ¾ cups whole wheat flour
- 2 teaspoons pumpkin spice blend (*see note)
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- ⅓ cup melted coconut oil
- ½ cup maple syrup or honey
- 1 cup pumpkin purée
- 2 eggs, room temperature
- ¼ cup milk
- 1 teaspoon vanilla extract
- ½ cup mini chocolate chips
Instructions
- Preheat oven to 350 degrees Fahrenheit. Grease muffin tin or line with paper muffin cups and set tin aside.
- Mix dry ingredients (flour, spices, baking powder, baking soda, and salt) together in a medium bowl.
- In a separate bowl, combine wet ingredients (melted oil, syrup, pumpkin purée, eggs, milk, and vanilla) in a large bowl.
- Add dry ingredients to wet ingredients and stir gently until batter is uniform. Add chocolate chips and stir to distribute evenly. Ensure no dry streaks of flour remain.
- Divide batter into muffin tins, filling 3/4 full.
- Bake at 350 degrees for 12-14 minutes, until a toothpick or skewer comes out mostly clean (a few crumbs are okay). If you're making regular-sized muffins, increase baking time to to 18-22 minutes.
Notes
In place of pumpkin pie spice, you can use the following: 1 teaspoon ground cinnamon, ½ teaspoon ground ginger, ¼ teaspoon ground nutmeg, and ¼ teaspoon ground allspice or cloves
Source: Adapted from Cookie + Kate. Adjusted several ingredients, added chocolate chips, and miniaturized muffins.
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Want more delicious muffin recipes? Try these:
- Healthy Apple Oatmeal Muffins
- Healthy banana chocolate chip muffins
- Mini blueberry muffins
- Corn dog muffins (a savory twist on muffins)

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