Love pumpkins in the fall but not sure how to use them? These easy pumpkin chocolate chip muffins are a deliciously wholesome treat your family is sure to enjoy, whether it’s for breakfast, a snack, or dessert. This recipe is not only gluten and dairy free but also uses no refined sugar, making it a healthier alternative for those mindful of ingredients. You can make this with fresh pumpkin puree in the fall or simply use canned pumpkin to enjoy this delightful flavor year-round! With warm spices like cinnamon and nutmeg complementing the rich chocolate chips, these muffins are the perfect way to celebrate the autumn season. Plus, they’re easy to whip up, ensuring that even on the busiest days, you can have a batch of these scrumptious muffins ready to savor and share.
Muffins are one of our favorite breakfast dishes here in the Young household. They are easy to pull together and are so delicious warm from the oven. We love to serve muffins paired with breakfast sausage and a bunch of our farm-fresh scrambled eggs.

Tips For Making Pumpkin Chocolate Chip Muffins
- If you use homemade pumpkin puree, consider adding a little bit more flour because homemade pumpkin puree tends to be much more watery than canned pumpkin. Try adding 2-3 Tbsp. of extra flour to balance out the extra moisture.
- Use coconut oil or avocado oil. These oils both tolerate higher temperatures well for baking. They are a good substitute for butter. You can use butter too, but I made this recipe to be specifically gluten and dairy free!
- Don’t over-fill muffin liners. This will result in dense, misshapen muffins.
Tools You May Need
Mixing bowls
Danish whisk
Muffin tins
Muffin liners
Ice cream scoop
Measuring cups and spoons
Baker’s Tips
Moist, fluffy muffins can be tricky to achieve. For the best results, I recommend mixing wet and dry ingredients separately and then mixing them together until just combined. Over-mixing the batter can result in dense muffins. This isn’t normally a problem with gluten free flours, but it is something to be aware of if you are using wheat flour!
If you are unsure about whether your muffins are baked through or not, just insert a toothpick into one and if it comes out clean then your muffins are ready. If there is batter on the toothpick then try giving your muffins a few more minutes until you test them again.
Honey can thicken over time and start to crystalize. If this happens, you can warm it up in a small saucepan with the coconut oil. Be sure to let it cool a bit before mixing it in with the eggs!
Gluten free baking can be tricky. I prefer to use a pre-mixed 1 for 1 baking flour that is made to act like your typical wheat flour. For baking, I recommend this option over using just one wheat flour alternative such as buckwheat or almond flour.
Ingredients For Pumpkin Chocolate Chip Muffins
Gluten Free Flour – I like Bob’s Red Mill GF 1 for 1 mix. King Arthur also has a good GF flour blend.
Baking Powder
Baking Soda
Real Salt – I use Redmond’s Real Salt
Cinnamon
Ginger
Nutmeg
Coconut Oil – Or avocado oil.
Honey – I buy mine from Azure Standard.
Eggs
Canned Pumpkin – Or you can use freshly made pumpkin puree
Chocolate Chips – I use Bake Believe semi-sweet chocolate chips for a dairy free, sugar free option.
How To Make Pumpkin Chocolate Chip Muffins
Preheat oven to 350 degrees Fahrenheit.
Grease muffin tins well or line with paper liners.
In a medium bowl, sift and mix together gluten free flour, baking powder, baking soda, real salt, cinnamon, ginger, and nutmeg. Set aside.
In a separate large bowl, whisk together canned pumpkin, melted coconut oil, honey, and eggs.
Gradually add dry ingredients to the wet ingredients and mix until just combined. Do not over-mix the dough as that will result in a dense muffin.
Fold in the chocolate chips.
Scoop batter into muffin tins and pop in the oven for 20-25 minutes or until muffins pass the toothpick test.
Let muffins cool and enjoy!
How To Store
Store muffins in an airtight container and use within 4-5 days. You can also store muffins in the freezer using a freezer safe container or zip-loc bag for up to 3 months.
Reheat muffins by placing them on a baking sheet and setting in the oven at 350 degrees Fahrenheit for 5-10 minutes or until completely warm.
Other Recipes From Little House Tending
Lemon Chicken Thighs with Creamy Coconut Rice
Salted Maple and Vanilla Latte
Gluten Free Pumpkin Chocolate Chip Muffins Recipe
If you try this recipe and enjoy it, I’d appreciate it if you would come back and leave a review and comment below. You can also save this recipe to Pinterest for a quick and easy reference!

Gluten Free Pumpkin Chocolate Chip Muffins
Equipment
- Mixing bowls
- Danish whisk
- Muffin tins
- Muffin liners
- Ice cream scoop
- Measuring cups and spoons
Ingredients
- 2 cups Gluten Free Flour Blend 330 g
- 1½ tsp Baking Powder 8 g
- ½ tsp Baking Soda 3 g
- ½ tsp Real Salt 4 g
- ¾ tsp Cinnamon 4 g
- ½ tsp Ginger 2 g
- ½ tsp Nutmeg 2 g
- ½ cup Coconut Oil 125 g
- ¾ cup Honey 245 g
- 2 Eggs
- 1 cup Canned Pumpkin 275 g
- ½ cup Chocolate Chips 80 g
Instructions
- Preheat oven to 350 degrees Fahrenheit.
- Grease muffin tins well or line with paper liners.
- In a medium bowl, sift and mix together gluten free flour, baking powder, baking soda, real salt, cinnamon, ginger, and nutmeg. Set aside.
- In a separate large bowl, whisk together canned pumpkin, melted coconut oil, honey, and eggs.
- Gradually add dry ingredients to the wet ingredients and mix until just combined. Do not over-mix the dough as that will result in a dense muffin.
- Fold in the chocolate chips.
- Scoop batter into muffin tins and pop in the oven for 20-25 minutes or until muffins pass the toothpick test.
- Let muffins cool and enjoy!
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