Gluten Free Pumpkin Muffins

Topped with gluten-free brown sugar streusel and pumpkin seeds, these gluten-free pumpkin muffins are a fall must-make. Super soft, with a tender crumb and the best texture, and spiced to perfection with warm fall spices you will catch yourself making this recipe over and over.

For more fall favorites and other gluten-free pumpkin recipes check out my Gluten Free Pumpkin Bread and my Gluten Free Pumpkin Scones.

Recipe Ingredient Notes

Gluten Free Flour: In this gluten-free pumpkin muffin recipe I use my gluten-free flour blend. I also tested this recipe with Bob’s Red Mill 1 – to 1 and King Arthur Measure for Measure Flour and both blends work great. All those blends mentioned already contain xanthan gum.

Almond Flour: The added almond flour gives these gluten-free pumpkin muffins not only their beautiful structure and crumb but also keeps them moist. If you prefer to make nut-free pumpkin muffins, please replace the almond flour with the same gluten free flour blend you use in this recipe. Make sure to use Almond Flour and not Almond Meal. Almond Meal is on the coarse side since it’s made from ground-up whole almonds. Almond flour is finely ground and blanched almonds. Since the skin of the almonds has been removed, almond flour is very fine, almost like a powder.

Greek Yogurt: Full Fat Greek Yogurt not only provides flavor in these Gluten Free Pumpkin Muffins but is also a binder that produces a thick batter. The thick batter tends to rise higher when baked. This means the muffins will have a beautiful bakery-style high-rise dome.

Canned Pumpkin: Make sure to use100% canned pumpkin and not pumpkin pie filling. They often sit next to each other on shelves at the grocery store and have very similar labels. As much as I love making everything from scratch, canned pumpkin is very convenient. Since this recipe doesn't use an entire can of pumpkin, make sure to check out my Pumpkin Spice Granola. A perfect way to use up leftover pumpkin.

Spices: You can either use storebought pumpkin pie spice or blend your own mix of ground cinnamon, ground ginger, nutmeg and cloves.

Streusel Topping

If you are like me, you may already have some leftover streusel in your freezer stashed away. You can either use that, top the muffins with raw pumpkin seeds before baking or follow this recipe to make a quick and easy Brown Sugar Streusel.

Combine the dry ingredients (sugar, flour, salt, cinnamon) in a large bowl and with a fork or your hands work in room temperature butter until it resembles crumbles. Make sure your butter is not too soft. It should not appear greasy. Store the crumble in the fridge until you are ready to use it. You can also make a bigger batch and freeze it.

How to make Gluten Free Pumpkin Muffin Batter

If you are like me, you love a quick and easy muffin recipe that comes together in a pinch. Just like my Gluten Free Blueberry Muffins and Gluten Free Banana Muffins, unsalted butter, large eggs, and greek yogurt do not need to come to room temperature. Using cold ingredients ensures the muffins bake into tall, bakery-style gluten-free pumpkin muffins.

Step 1: Line the muffin pan with 8 muffin liners and set aside. These liners are sometimes called Muffin Cups or Cupcake liners. This recipe makes 8-10 muffins, depending on how full you fill the liners.

Step 2: Sift together gluten-free flour, almond flour, brown sugar, granulated white sugar, baking powder, baking soda, kosher salt, and spices in the bowl of the stand mixer.

Step 3: Cut the cold, unsalted butter into small pieces and add to the dry ingredients. Mix at a low speed until it resembles a coarse meal. The hunks of butter should not be bigger than the size of peas.

Step 4: In a separate bowl whisk together the pumpkin puree, greek yogurt, eggs, and vanilla extract until smooth.

Step 5: With the mixer running on low, combine the wet ingredients with the dry ingredients. Mix until a thick batter forms.

How to bake Gluten Free Pumpkin Muffins

Step 1: Using a large cookie scoop (like this #20 scoop) equally divide the gluten free pumpkin muffin batter between the muffin liners.

Step 2: Top each muffin with some brown sugar streusel or raw pumpkin seeds. Gently press the streusel and/or the pumpkin seeds on top of the muffins to ensure it sticks to them.

Step 3: Place the gluten-free muffins in the fridge while your oven preheats to 350F. Allowing the batter to rest, even if it’s just 15-30 minutes will help hydrate the flour which builds a better crumb. Also – cold muffin batter will rise higher!

Step 4: Bake the pumpkin muffins at 350F for 24-27 minutes until they are golden brown. I always check the doneness after 24 minutes. The muffins are done when until they are golden brown and a toothpick inserted in the center comes out clean. Make sure not to overbake them. That will cause them to dry out. Baking times depend on how many muffins you divided the batter into and your oven. Smaller Muffins bake faster while larger muffins clearly take longer to bake.

Step 5: Allow the gluten-free pumpkin chip muffins to cool in the muffin pan for 5-10 minutes before transferring them to a wire rack/cooling rack. I use a spoon or a butter knife to remove them from the muffin pan. Yes, there will be some “loose streusel” which makes a fabulous snack. If you allow them to cool completely in the muffin tin, the heat can’t escape and the muffin papers will be soggy.

Allow the gluten-free pumpkin muffins to cool completely on a wire rack.

Storage & Freezing

Gluten-Free Pumpkin Muffins tend to be very moist and have the tendency to become soggy if they sit for an extended period of time in an airtight container. To avoid this, I recommend placing a sheet of paper towels on the bottom of the container before adding the fully cooled pumpkin muffins. Top with another piece of paper towel before putting the lid on the container. The paper towels will act as a sponge and will absorb moisture.

This storage trick can be applied to all of my muffin and quick bread recipe found on my website.

Store the muffins in an airtight container for 2-3 days. If the paper towels become damp, I recommend replacing them.

To freeze the gluten-free muffins, place them on a sheet tray and pop them in the freezer for 30-45 minutes or until they are solid. Once frozen transfer them to an airtight container or freezer bag. Freeze for up to 3 months. When ready to eat, allow for them to thaw at room temperature or nuke in the microwave for 15-30 seconds.

How to make Pumpkin Puree

Canned pumpkins can be difficult to find outside of the US. BUT, butternut squash should be available. Which is the perfect substitute for pumpkin. You will need a medium-sized butternut squash (around 24oz/700 grams), a sheet tray, an oven, and a food processor or blender.

Preheat to 400F/200°C. Split the butternut squash lengthways, remove seeds, and place cut-side down on a foil-lined aluminum baking sheet. Roast it until fork-tender which can take about 45 minutes depending on the size of the squash and your oven. Remove it from the oven and allow for it to cool until you can handle it.

Remove the “flesh” from the squash and puree it with a food processor or blender. Use this in the recipe. Please be aware, that sometimes homemade pumpkin puree is “wetter” than canned pumpkin. So you may need to plot it with some paper towels to remove the moisture.

Pumpkin Puree vs Canned Pumpkin Pie Filling

As the name indicates, canned pumpkin pie filling should be used to make pies. It is presweetened and contains all the spices which makes it harder to work with in a recipe like Gluten Free Pumpkin Muffins.

Does Libby's canned pumpkin contain gluten?

Good news! Libby's canned pumpkin is made with just one ingredient: pumpkin. It does not contain any preservatives, is vegan and gluten-free It is also a good source of Vitamin A and fiber.

Suggestions on how to make Gluten Free Vegan Pumpkin Muffins

If you are on a gluten free and dairy free diet you may be curious about how to make this pumpkin muffin recipe dairy-free and egg-free. Please be aware that any ingredient changes will change the flavor and texture of the end product.

The butter used in this recipe can be replaced equally with dairy-free butter or coconut oil as long as it is solid. As an egg substitute, I recommend using 100 grams of unsweetened apple sauce. The muffins will not be as light and fluffy as muffins made with eggs.

Note about Salt in my Recipes

I use Diamond Kosher Crystal Salt in all of my recipes unless otherwise stated. If use use a different brand or kind of salt in your kitchen please adjust accordingly since some salts can be saltier. If you use Morton’s Kosher Salt please be aware that their salt granules are smaller in size, denser, and crunchier and twice as salty.

Baking in grams

I share my recipes in grams and by weight since baking by weight is the most accurate way to bake. Digital Scales are very affordable and easy to use. You can purchase them on Amazon for less than a set of measuring cups. For small amounts under 10 grams, I like to use this Precision Pocket Scale. Measuring cups are very inaccurate which can cause significant errors when it comes to gluten-free baking or baking in general. Especially since I bake with gluten-free flours which weigh differently than “regular” flours. I do provide some ingredients like spices and leavening agents in measuring spoons. To learn more about Baking with a digital scale, make sure to check out my post about Baking by weight.

Note about Ovens and Oven Temperatures

All my recipes are tested and developed with a conventional oven. I always bake my baked goods on the rack placed in the MIDDLE of my oven. This way the heat coming from the bottom will not burn my baked goods.

If you are baking with convection (fan-forced), please adjust the recipes accordingly. Convection oven can cause baked goods to dry out quickly and still be raw inside. Since takes at least 15-20 minutes for a standard American Oven to be fully preheated. I highly recommend investing in an Oven Thermometer.

Substitutions and Modifications

Any dietary or ingredient modifications/substitutions to this recipe may alter the end result in appearance and taste. I test my recipes several times as published in this post and The Gluten Free Austrian Blog is not responsible for the outcome of any recipe you find on our website.