These gluten-free pumpkin muffins have a lot going for them! Not only GF, they’re also oil-free, grain-free, dairy-free, and made in one bowl. Almond flour makes up the base here, for a delicious lightly sweet snack.
By using non-dairy yogurt and a touch of arrowroot flour, the number of eggs can be reduced (two, instead of the usual three or four), in turn reducing any eggy flavour that can be so unpleasant in gluten-free baking.
With warm spices, walnuts, and chocolate combined with the pumpkin, these are quintessentially autumn in flavour. A slight caramel flavour from coconut sugar adds even more, and all combined makes for almond flour muffins that are both light and a good, filling, snack.

Why You Should Try This Recipe
We all love the combination of pumpkin and warm spices in autumn, and this is another way to get those flavours in healthier muffin form.
- It’s a one-bowl recipe: everything is mixed in the same bowl, which means less dishes for you.
- Made with just one flour: no faffing around with a bunch of expensive flour types – you really only need almond flour. Arrowroot or cornstarch is a good addition but not completely mandatory.
- Less eggs, more flavour: you should be able to taste the pumpkin and spices, and here you can. The eggs don’t overwhelm and there’s a bit more sweetness from the yogurt.
- High protein: one muffin has about six grams of protein, so a snack should keep you full longer.
Ingredients

Ingredient Notes and Substitutions
- Almond Flour: be sure to use almond flour, and not almond meal, for this recipe. I found that blanched almond flour made for the most attractive muffins, but it doesn’t really matter.
- Pumpkin Puree: homemade or canned. Homemade pumpkin puree is often slightly more liquid than canned (and tastes better). I haven’t tested this recipe with canned puree but it should simply make the muffins slightly more solid, which is fine.
- Eggs: there isn’t a good vegan version of these muffins. The eggs are integral to the texture and structure, and subbing something like flax or aquafaba doesn’t have similar results. Sub at your own risk.
- Coconut Sugar: I have tested these with maple syrup and honey instead of coconut sugar. While the muffins turn out fine with these substitutions, they’re not the best. You can make them with a liquid sweetener but the texture will be less pleasant, though the colour is more orange.
- Yogurt: thick, Greek-style coconut yogurt is ideal, but any unsweetened non-dairy yogurt can be used. You can find a coconut yogurt recipe in the Occasionally Eggs Cookbook.
- Starch: arrowroot flour can be omitted. It adds a bit of heft and makes the muffins a bit more muffin-y, but they’re still excellent without. Sub with an equal amount tapioca starch, or half the amount if using cornstarch.
Step by Step
1. Mix the eggs: whisk the eggs well in a large mixing bowl.
2. Add the other wet ingredients: add the pumpkin and yogurt, and mix again to combine.

3. Add the dry ingredients: and mix very well. No streaks of flour should be visible.
4. Mix in the nuts and chocolate: now you can fold in the add-ins, incorporating evenly.
5. Scoop into forms: divide evenly between lined muffin cups.
6. Bake: bake the muffins for about 22 minutes, until they pass a toothpick test.

Recipe Notes
The muffins will stick to the paper liners until they’ve cooled completely. If they’re still warm, you’ll lose quite a bit when peeling off the liner. After a couple hours of chilling, they shouldn’t stick at all. I haven’t tried greasing the tin instead of lining but it should work.
They look as though cocoa is added, but it’s the combination of coconut sugar and spices that make them look darker. This is why I tested with liquid sweetener, but they’re best with coconut sugar.
The texture is moist and slightly spongey, not dry and cake-y. It’s a bit personal based on what you like, but if you love a very tender muffin, then these almond flour pumpkin muffins are perfect.
How to Store
Storage: refrigerate for up to five days in a sealed container. I recommend refrigerating as these do spoil quickly at room temperature.
Freezing: cool fully before freezing in an airtight container for at least a month. Thaw in the refrigerator before serving.

Expert Tips
- Use accurate measurements: as with any baking, but gluten-free recipes in particular, I highly recommend using accurate weight measurements, although cups are provided in the recipe card.
- Check oven temperature: this is a common problem. Home ovens often run 10-20°C off from what they’re set at (I’ve had an oven that was often 50°C too hot!) so a small oven thermometer works wonders. If you find that your bakes are often failing despite following the recipe exactly, you may need to check this.
- Mix all you’d like: don’t worry about over-mixing, as you would with muffins containing gluten. Mix until no streaks of flour are visible.
More Almond Flour Recipes
Almond Flour Brownies
Almond Chocolate Chunk Cookies
Gluten-Free Ice Cream Sandwiches
More Pumpkin Desserts
Vegan Pumpkin Cinnamon Rolls
Chocolate Pumpkin Cupcakes
Vegan Pumpkin Cookies
If you make these Gluten Free Pumpkin Muffins or any other snack recipes on Occasionally Eggs, please take a moment to rate the recipe and leave a comment below. It’s such a help to others who want to try the recipe. For more OE, follow along on Instagram, Facebook, and Pinterest, purchase the Occasionally Eggs cookbook, or subscribe for new posts via email.
Gluten Free Pumpkin Muffins
Ingredients
- 2 large eggs
- 220 grams pumpkin puree
- 120 grams coconut yogurt
- 180 grams almond flour
- 100 grams coconut sugar
- 2 tablespoons arrowroot flour
- 1 teaspoon baking soda
- 2 teaspoons cinnamon
- ½ teaspoon nutmeg freshly grated – halve if using ground
- ¼ teaspoon ground ginger
- ¼ teaspoon sea salt
- 50 grams raw walnuts roughly chopped
- 50 grams dark chocolate roughly chopped
Instructions
- Preheat the oven to 180°C (350°F) and line a 12-cup muffin tin with paper liners.
- Add two eggs to a large mixing bowl and whisk until foamy.2 large eggs
- Add 220 grams (3/4 cup) pumpkin puree and 120 grams (1/2 cup) yogurt, and whisk again to mix.220 grams pumpkin puree, 120 grams coconut yogurt
- Add 180 grams (1 3/4 cups) almond flour, 100 grams (1/2 cup) coconut sugar, 2 tablespoons arrowroot flour, 1 teaspoon baking soda, 2 teaspoons cinnamon, 1/2 teaspoon nutmeg, 1/4 teaspoon ginger, and 1/4 teaspoon salt to the bowl. Whisk until a well combined and no streaks of flour remain (don’t worry about over-mixing).180 grams almond flour, 100 grams coconut sugar, 2 tablespoons arrowroot flour, 1 teaspoon baking soda, 2 teaspoons cinnamon, 1/2 teaspoon nutmeg, 1/4 teaspoon ground ginger, 1/4 teaspoon sea salt
- Fold in 50 grams (1/4 cup) of walnuts and 50 grams (1/4 cup) of chocolate.50 grams raw walnuts, 50 grams dark chocolate
- Divide the batter equally between the prepared muffin cups.
- Bake for 22-24 minutes, or until browned and a toothpick inserted into the centre of a muffin comes out clean. The muffins will puff up significantly and then fall a bit, this is normal.
- Refrigerate in a sealed container for up to five days, or freeze to up to a month. I recommend keeping these chilled as they spoil quickly.
Video
* For American cup measurements, please click the pink link text above the ingredient list that says ‘American’.
Nutrition
Nutrition is provided as a courtesy and is an estimate. If this information is important to you, please have it verified independently.
Bear McGuinness says
These look delicious! Thank you! The photos are wonderful, too, especially the before and after shots. So helpful.
Alexandra Daum says
Happy to hear that, thanks so much!