Made with wholesome oat flour, these gluten-free pumpkin muffins are incredibly moist and full of classic pumpkin spice flavor. Tart cranberries and melty chocolate chips add the perfect contrast and take this easy fall recipe to a new level!

Quick Look at the Recipe
- 🍽️ Flavor: Rich pumpkin spice contrasted with tart cranberries and chocolate.
- ⏱️ Prep Time: 10 minutes
- 🔥 Cook Time: 24 minutes
- 🕒 Ready In: 1 hour and 6 minutes (including 30 minutes of resting time)
- 👥 Servings: 12 muffins
- 🥣 Main Ingredients: Oat flour, pumpkin puree, cranberries, chocolate chips
- 📖 Dietary Info: Gluten-free, refined sugar-free option, dairy-free option
- ❄️ Freezer Friendly: Yes!
- 👩🍳 Tip: Yogurt is the special ingredient that adds a richer flavor and moist texture to these gluten-free muffins.

The Ultimate Secretly Healthy Muffins
Healthy(ish) fall baked goods are my ultimate weakness, and pumpkin, cranberries, and chocolate might just be the best flavor combination of all! In my mission to create clean-eating recipes that taste every bit as delicious as the traditional versions, I’ve been perfecting these muffins for years.
They’re incredibly moist, rich with warm flavor, and finally ready to share. I’m pretty sure they’ll become a yearly (if not weekly) tradition in your home, just like they are in ours!
What Makes these Gluten-Free Muffins Special?
- Soft, moist texture that won’t spoil the secret that they’re gluten free!
- Rich and complex flavor with plenty of warm pumpkin spice, tart cranberries, and sweet chocolate.
- Healthier muffin recipe made with oat flour and a natural sweetener.

Ingredients
Tools Needed
Step-By-Step Instructions

Step 1: First, in a large mixing bowl, whisk together the wet ingredients: pumpkin puree, yogurt, coconut sugar, eggs, apple cider vinegar, and vanilla.

Step 2: Next, in another bowl, whisk together the oat flour, baking soda, cinnamon, nutmeg, ginger, cloves, and salt.

Step 3: Then add the dry ingredients to the wet ingredients and stir until just combined.

Step 4: Gently fold in the cranberries and chocolate chips (if you’re including them). Then cover the bowl and place the batter in the fridge to rest for 30 minutes.

Step 5: Preheat your oven to 350 degrees and grease your muffin pan. Alternatively, you can line it with baking cups instead. Then evenly divide the batter between the muffin cups.
Bake for 24-28 minutes or until a toothpick inserted into the center of a muffin comes out mostly clean with a few moist crumbs.
Allow the muffins to cool for about 10 minutes before removing them from the pan.

If you’re looking for more gluten-free muffin recipes, check out my oat flour apple muffins and classic gluten-free banana muffins!
Tips for Success
Don’t over-mix – For soft, tender muffins, stir the batter until just combined. It’s better to slightly under-mix, so don’t worry if you still see a few tiny bits of flour. That will get stirred in when you fold in the cranberries and chocolate chips.
Allow time to rest – This is a huge key to moist oat flour baked goods!
Let cool in the pan – For perfectly done muffins that pop out of the pan cleanly, make sure to let them cool in the pan for about 10 minutes before removing them.

FAQs
Store gluten-free pumpkin muffins on a plate wrapped in plastic wrap, in a gallon ziplock bag, or airtight container at room temperature for 3-5 days.
Yes, pumpkin muffins freeze wonderfully in an airtight container or plastic freezer bag for 2-3 months.
Yes, this pumpkin batter makes delicious bread! Simply divide between 2 bread pans and bake for 40-45 minutes. For detailed instructions, see my oat flour pumpkin bread recipe.
Yes, you can use dried cranberries in pumpkin muffins, however, fresh cranberries are more flavorful and give the muffins a better texture.
No, these pumpkin cranberry muffins are created specifically for oat flour, and other types of flour won’t create the same good result.
If you try this recipe, let me know in the comments! Tag me on Instagram @violet_rightathome

Gluten-Free Pumpkin Muffins
Equipment
Ingredients
- 3 cups oat flour certified gluten free
- 15 ounces pumpkin puree not pumpkin pie filling
- 1 1/4 cups cranberries
- 3/4 cup coconut sugar
- 3 eggs
- 1/3 cup yogurt dairy or non-dairy
- 1 1/2 teaspoons baking soda
- 1 1/2 teaspoons ground cinnamon
- 1 teaspoon apple cider vinegar
- 1 teaspoon nutmeg
- 1 teaspoon vanilla extract
- 1/4 teaspoon cloves
- 1/4 teaspoon ground ginger
- 1/4 teaspoon salt
- 1/3 cup chocolate chips optional
Instructions
- In a large mixing bowl, whisk together the pumpkin puree, yogurt, coconut sugar, eggs, apple cider vinegar, and vanilla.15 ounces pumpkin puree, 3/4 cup coconut sugar, 3 eggs, 1/3 cup yogurt, 1 teaspoon apple cider vinegar, 1 teaspoon vanilla extract
- In another bowl, whisk together the oat flour, baking soda, cinnamon, nutmeg, ginger, cloves, and salt.3 cups oat flour, 1 1/2 teaspoons baking soda, 1 1/2 teaspoons ground cinnamon, 1 teaspoon nutmeg, 1/4 teaspoon cloves, 1/4 teaspoon ground ginger, 1/4 teaspoon salt
- Add the dry ingredients to the wet ingredients and stir until just combined
- Fold in the cranberries and chocolate chips (if you're including).1 1/4 cups cranberries, 1/3 cup chocolate chips
- Cover and place the batter in the fridge to rest for 30 minutes.
- Preheat your oven to 350 degrees and grease a 12 cup muffin pan or line with baking cups.
- Evenly divide the batter between the muffin cups.
- Bake at 350 degrees for 24-28 minutes or until a toothpick inserted into the center of a muffin comes out mostly clean with a few moist crumbs.
- Cool for about 10 minutes before removing from the pan. Enjoy!
Notes
- You can substitute brown sugar for the coconut sugar.
- Store at room temperature for 3-5 days or freeze for 2-3 months.
Nutrition
If you tried these healthy pumpkin muffins, I’d love to hear how they turned out for you! Please make sure to come back and leave a comment and a ⭐️⭐️⭐️⭐️⭐️ rating.


These rich pumpkin muffins are a fall favorite around here! If you try them I think they’ll become a favorite in your home too!