Small-Batch Gluten-Free Pumpkin Chocolate Chip Muffins
- Our Nourished Kitchen
- 5 days ago
- 5 min read
Updated: 5 days ago
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I love when the weather starts to cool down, the days get a little shorter, and the leaves begin to turn shades of amber. This time makes me crave warm, comforting treats like these Small-Batch Gluten-Free Pumpkin Chocolate Chip Muffins.
Why You'll Love this Small-Batch Gluten-Free Pumpkin Chocolate Chip Muffins
Intentionally, I like to make small batches of treats for my family. Everyone gets to have a muffin or two, and the scarcity keeps them special. These fluffy gluten-free pumpkin muffins are packed with pureed pumpkin, brown sugar, warm pumpkin pie spice, and chocolate chips. They have tall domed bakery-style muffin tops and a moist gluten-free muffin crumb. I used a combination of 1:1 gluten free flour and almond flour. This combination of flours creates a moist, delicious muffin crumb. If you prefer to keep these treats as dairy-free chocolate chip pumpkin muffins, you can use dairy-free chocolate chips. However, regular semi-sweet or milk chocolate chips will also work great in this recipe!
The exact Gluten-Free Flour Blend I used in these Small-Batch Gluten-Free Pumpkin Chocolate Chip Muffins:
A bag of Better Batter Gluten Free 1:1 Flour A bag of Bob's Red Mill Superfine Almond Flour
Check out Shop My Kitchen Essentials for other great gluten-free cooking products and non-toxic kitchenware I use in my home.
Recipe FAQs
Can I let the muffin batter rest longer than 20 minutes?
Yes, up to 30 to 45 minutes total is completely fine and actually helps the flours hydrate even better. However, resting longer than 1 hour can cause the leavening reaction (baking soda + apple cider vinegar) to lose it's lifting power, resulting in a denser muffin.
Why is there apple cider vinegar in a muffin recipe, and does the muffin taste like vinegar?
No, you won't taste it at all--apple cider vinegar gives baking soda a major power boost to help the muffins rise high. It helps you get tall, fluffy muffin tops instead of flat, heavy ones.
How do I get my muffins to rise into tall bakery-style domes?
To get tall bakery-style domes, rest the batter to thicken it, fill the muffin cups to the top, and start with a 5-minute initial blast of high heat at 425°F before lowering the temperature to 350°F. The initial blast of steam helps the muffins rise quickly.
Why did my gluten-free pumpkin chocolate chip muffins turn out gummy in the middle?
Too much moisture in the pureed pumpkin is likely the cause. If your pumpkin puree looks watery, blot it gently with a paper towel before measuring. Additionally, ensure you measure flour by fluffing and spooning it into measuring cups, then leveling it off-- rather than scooping directly from the bag.
Why did my chocolate chips sink to the bottom?
Thin batter allows heavy chocolate chips to fall to the bottom before the structure sets in the oven. Letting the batter rest for 15–20 minutes thickens it enough to keep the chips suspended throughout the muffin. The batter should look and feel very fluffy after the rest.
Can I use fresh pumpkin puree instead of canned?
I have not tried this recipe with fresh pumpkin. Canned pumpkin puree is highly recommended. Fresh homemade pumpkin puree can have more moisture, which can weigh down gluten-free batter and make the muffins dense or gummy. If using fresh puree, strain it through cheesecloth or a fine-mesh strainer overnight to remove any extra water.
Can I substitute the almond flour if I have a nut allergy?
Yes you can. Super-fine almond flour adds essential moisture and healthy fats to gluten-free baking. If you have a nut allergy, you can swap the almond flour for an equal amount of oat flour or additional 1:1 gluten-free baking flour. Keep in mind the muffins may turn out slightly less tender.
Can I double this recipe to make 12 muffins?
Yes, this recipe scales up easily! Simply double all ingredient quantities. When baking a full batch of 12 in a single pan, you won't be able to alternate empty cups, but the high-temperature start (425°F for 5 minutes) and 15–20 minute batter rest will still yield great height.
How should I store these fluffy gluten-free pumpkin muffins?
Store them in an airtight container at room temperature lined with a paper towel to absorb excess moisture for up to 3 days (if they last that long), or freeze individual muffins for up to 3 months.
Substitutions & Customizations
Nut Free
Swap equal parts oat flour or additional 1:1 GF flour for a nut-free version (add 1 tsp extra oil if using 1:1 flour).
Refined Sugar Free
Swap brown sugar at a 1:1 ratio with coconut sugar or maple sugar. This will add warm caramel notes.
DIY Pumpkin Spice
Combine together 1 tsp cinnamon + ¼ tsp nutmeg + ¼ tsp ginger + ⅛ tsp ground cloves
Mix-in Variations
Swap 1/2 the chocolate chips for toasted chopped pecans, walnuts,
pumpkin seeds (pepitas), or dried cranberries.
Check out other great gluten-free, dairy-free recipes to add to your weekly rotation:
If you try this recipe, leave a comment below👇 and let me know how it turned out—I absolutely love hearing from you!
How to Make this Small-Batch Gluten-Free Pumpkin Chocolate Chip Muffins
Step 1: Prep Muffin Pan:
Line a 6-cup standard muffin pan with parchment paper liners or grease thoroughly. If you are doing a double recipe, add liners or grease all 12-cups.
Step 2. Whisk Dry Ingredients
n a medium bowl, whisk together the 1:1 gluten-free flour, almond flour, baking powder, baking soda, pumpkin pie spice, and salt until smooth and lump-free.
1:1 gluten-free flour, almond flour, baking powder, baking soda, pumpkin pie spice, & salt in a bowl 1:1 gluten-free flour, almond flour, baking powder, baking soda, pumpkin pie spice, & salt mixed
Step 3. Whisk Wet Ingredients
In a separate large bowl, whisk the pumpkin puree, sugar, oil, egg, 2 tsp vanilla extract, and apple cider vinegar until fully combined.
A bowl with pumpkin puree, sugar, oil, egg, 2 tsp vanilla extract, and apple cider vinegar A bowl with the dry ingredients and the mixed wet ingredients
Step 4. Combine the Wet and Dry
Add the dry mixture to the wet ingredients and fold with a rubber spatula just until combined. Gently fold in the chocolate chips.
A bowl of dry mixture and wet mixture for pumpkin chocolate chips muffins Combining the dry mixture and wet mixture with a spatula The pumpkin batter base and a scoop of chocolate chips A bowl of pumpkin chocolate chips muffin batter
Step 5. Rest Batter
Cover the bowl and let the batter sit at room temperature for 20 minutes.
Step 6. Preheat Oven and Scoop
Set oven to 425°F. Fill muffin cups to the very top with batter. You should have enough to fill all 6 to the very top. Press the reserved 2 tablespoons of chocolate chips onto the tops.
A bowl of fluffy, rested gluten free pumpkin chocolate chip muffin batter with a large scoop Scooped Gluten-Free Pumpkin Chocolate Chip Batter in Muffin Cups with Parchment Liner
Step 7. Bake
Bake at 425°F for 5 minutes then without opening the oven door, lower the temperature to 350°F and bake for another 14 to 16 minutes until a toothpick or sharp knife comes out clean.
Step 8. Cool
Leave the muffins in the pan for 5 minutes, then transfer them immediately to a wire cooling rack.
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