Gluten Free Pumpkin Cream Cheese Muffins

These Gluten Free Pumpkin Cream Cheese Muffins are a delicious twist on a classic fall favorite. Think of them as a homemade version of the popular Starbucks Pumpkin Muffins. The spiced pumpkin muffin pairs perfectly with a smooth, tangy cream cheese center and a crunchy pumpkin seed streusel. Whether you're enjoying them for breakfast, dessert, or as a cozy snack, these muffins are sure to become a family favorite.

Recipe Ingredient Notes

Gluten Free Flour: I’ve tested this muffin recipe with my own gluten free flour blend, Bob’s Red Mill 1-to-1 and King Arthur Measure for Measure, and all three deliver fantastic results. That said, other flour blends might work just as well—I just haven’t tested them yet. Keep in mind that the blends I used to perfect this recipe do contain xanthan gum.

Almond Flour: These gluten free pumpkin cream cheese muffins owe their perfect structure and tender crumb to the addition of almond flour, which also helps keep them moist. Want to make them nut-free? Simply swap the almond flour for more of the gluten-free flour blend used in this recipe. (Pro Tip: Check the baking aisle at your local Aldi – their Almond flour is exceptional and very affordable)

Sour Cream: Sour cream isn’t just for flavor in these gluten-free pumpkin cream cheese muffins - it also acts as a binder, creating a thick batter. This thicker batter helps the muffins rise higher during baking, resulting in gorgeous, bakery-style domed tops. Sour Cream can be replaced with Greek Yogurt.

Pumpkin Puree: Be sure to use 100% pure canned pumpkin, not pumpkin pie filling—the two are often side by side on store shelves with similar labels. While homemade pumpkin puree is wonderful, canned pumpkin is incredibly convenient for this recipe.

Pumpkin Seeds: I use raw pumpkin seeds for the streusel. They add a delightful crunch and a subtle nutty flavor to brown sugar streusel, taking it to the next level.

Equipment needed to make Pumpkin Cream Cheese Muffins

This recipe for Gluten Free Pumpkin Cream Cheese Muffins does not require any fancy tools but you will need a few basic tools to successfully make this recipe. I like to mix the muffin batter with my stand mixer while I mix the cream cheese filling with a hand mixer. But you can also make both in the stand mixer.

A Muffin tin: I use a regular-sized muffin tin for this recipe which holds 12 regular-sized muffins/cupcakes.

Muffin Liners: You can either use regular-sized muffin/cupcake liners for this recipe or make your own muffin liners. You can find a video and instructions on how to make muffin liners here: How to make Muffin Liners with Parchment Paper

Portion scooper: The easiest way to portion out muffins is by using a large scooper. I use the same yellow scoop I use to portion out cookies to portion out my muffin batter.

Additional tools needed: A digital kitchen scale, a whisk, a spatula, two bowls, sifter to sift together dry ingredients. You will also need a ziplock bag or a piping bag to pipe the cream cheese filling into the pumpkin muffin batter.

Pumpkin Seed Streusel Topping

1. Start by melting the butter in a small pot on the stove or in a microwave-safe bowl. Allow it to cool for a few minutes.
2. While the butter is cooling, combine gluten free flour, light brown sugar, pumpkin seeds, cinnamon, and kosher salt in a mixing bowl. Whisk these ingredients together. If you like you can replace the ground cinnamon with some pumpkin pie spice.
3. Using a fork or a small spatula, gently blend the dry ingredients with the melted butter until crumbles start to form. Be careful not to overmix.
4. Place the pumpkin seed streusel topping in the refrigerator while you prepare the gluten free muffin batter for the pumpkin muffins. You can also freeze the crumb topping for up to 3 months. It's a versatile addition that works well in muffins, coffee cakes, and even cheesecakes.

Cream Cheese Filling

Make sure the cream cheese is at room temperature before making the filling. I like to slice the block of cream cheese into smaller chunks and place them on a plate. Smaller pieces soften much faster than a whole block. It should take about 15-20 minutes at room temperature.

1. To make the cream cheese filling, combine the room temperature cream cheese, powdered sugar, salt, and a generous teaspoon of vanilla extract in a medium bowl, and with an electric hand mixer mix to combine. You may also do this in your stand mixer using the paddle attachment. Mix until light and fluffy.
2. Transfer the cream cheese filling to a piping bag or a ziplock bag. Set aside until the muffins are ready to be assembled.

How to make Gluten Free Pumpkin Muffin Batter

There’s no need to bring the unsalted butter, eggs, or sour cream to room temperature for this recipe. Using cold ingredients helps create a thick batter that bakes into tall, bakery-style gluten free pumpkin muffins with beautiful domed tops.

1. Line the muffin pan with 12 muffin liners and set aside. You can either use regular-sized muffin/cupcake paper liners for this recipe or make your own muffin liners. You can find a video and instructions on how to make muffin liners here: How to make Muffin Liners with Parchment Paper
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.
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 for about 2-3 minutes. The hunks of butter should not be bigger than the size of peas. If there are some little chunks of butter, it's okay!
4. In a separate bowl whisk together the pumpkin puree, sour cream, large eggs, and vanilla extract until smooth.
5. With the mixer running on low, combine the wet ingredients with the dry ingredients. Mix until a thick batter forms.
6. Use a flexible spatula to gently fold the pumpkin muffin batter a few times, ensuring all the ingredients are fully incorporated. Check the bottom of the mixing bowl to make sure no dry ingredients are hiding there. You want a smooth, well-mixed batter for the best results!

How to bake Gluten Free Cream Cheese Muffins

1. Using a large cookie scoop (like this #20 scoop), evenly divide the gluten-free pumpkin muffin batter between the muffin liners, filling each one all the way to the rim. The batter may be a bit stiff, so it might take a little extra effort to get it into the liners.
2. Next, grab your prepared cream cheese filling. Snip off the corner of the ziplock bag or the tip of the piping bag.
3. Insert the piping bag tip into the center of each muffin and pipe 2-3 teaspoons of cream cheese mixture into the middle, making sure to get the cheesecake filling about halfway into the batter. Leave a small dollop of cream cheese on top of the muffin for that perfect, creamy crown.
4. Top each muffin with a generous amount of streusel. Use your hands to gently press it on top of your muffin batter. At this point, you can refrigerate the pumpkin cheesecake muffins for up to 48 hours before baking them.
5. Place the gluten free muffins in the fridge while your oven preheats to 425F. 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!
6. Once the oven is fully preheated, bake the pumpkin cream cheese muffins for 7 minutes at 425F. After 7 minutes reduce the oven temperature to 365F (without opening the oven door) and continue to bake the muffins for 18-20 minutes or until a toothpick comes out *almost* clean. Make sure to poke the muffin with the toothpick and not the cream cheese center. Baking times depend on how many muffins you divide the batter into and your oven. Smaller Muffins bake faster while larger muffins take longer to bake.
7. Let the gluten free pumpkin cream cheese muffins cool in the pan for 5-10 minutes. Then transfer them to a wire rack to cool completely. I use a spoon or a butter knife to gently lift them out of the muffin pan. Don’t worry if some of the streusel falls off - it makes for a delicious snack!

Storage & Freezing

If you plan to eat the pumpkin muffins within a couple of days, store them in an airtight container at room temperature. This helps keep the muffins soft and fresh.

If your kitchen is on the warmer side, store them in the refrigerator. Place them in an airtight container or cover them tightly with plastic wrap to prevent them from drying out. They’ll stay fresh for about 5-6 days.

To store muffins for longer, freezing is a great option. First, allow the muffins to cool completely. Then, place them on a sheet tray and freeze for 30-45 minutes, or until they are solid. Once frozen, transfer the muffins to an airtight container or freezer bag. They’ll stay fresh in the freezer for up to 3 months.

When you’re ready to enjoy them, let them thaw at room temperature or in the fridge overnight. For a quicker option, you can microwave them for 15-30 seconds to speed up the thawing process.

FAQ - Gluten Free Pumpkin Cream Cheese Muffins

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.