Gluten Free Carrot Cake Muffins with Cream Cheese Filling

If you love carrot cake, these Gluten Free Carrot Cake Muffins with Cream Cheese Filling are going to be right up your alley. They’re soft, perfectly spiced, and filled with a simple cream cheese center that gives each bite that classic carrot cake taste. They’re perfect for breakfast, brunch, or an afternoon treat.

Recipe Ingredient Notes

Gluten Free Flour: I have this recipe for Gluten Free Carrot Cake Muffins with Cream Cheese Filling with my homemade gluten-free flour mix, Bob’s Red Mill 1-to-1 (blue bag), and King Arthur Measure for Measure. Each one baked up with a beautiful, light crumb, but my personal favorite for this recipe was Bob’s Red Mill. While I haven’t tried other blends, I imagine many would work well here too. Just make sure the gluten free flour mix does contain xanthan gum (or guar gum).

Carrots: Peel and finely grate your carrots for the best texture and flavor. I avoid pre-shredded carrots from the grocery store, as they tend to be dry and less flavorful.

Oil: I use grapeseed oil here, but a neutral oil such as vegetable oil or even a mild olive oil will work just fine.

Milk: I like to use whole milk in this recipe, but any milk you have on hand or even water will work. I haven’t tested it with dairy-free alternatives, but I don’t see a reason they wouldn’t work as well.

Spices: To capture that classic carrot cake flavor, I use a blend of ground cinnamon, ground ginger, and nutmeg. Feel free to adjust the spices to suit your personal taste. If you are a fan of cloves, feel free to add about ⅛th of a teaspoon (a little goes a long way here)

Cream Cheese: For the cream cheese filling I recommend using a full fat block style cream cheese.

Gluten Free Oats: I use certified gluten free oats in my oat streusel topping. If you choose not to use oats here, feel free to add some chopped nuts such as pecans or walnuts instead.

Gluten Free Oat Streusel

If you choose not to eat gluten free oats, feel free to replace the oats with chopped up pecans or walnuts.

1. Step 1: Melt the unsalted butter in a small pot on the stove or in a microwave-safe bowl. Allow it to cool for a few minutes. Dairy-Free Butter works great here.
2. Step 2: While the butter is cooling, combine gluten free flour, light brown sugar, rolled gluten free oats, cinnamon, and kosher salt in a mixing bowl. Whisk these ingredients together.

3. Step 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 it.
4. Step 4: Place the gluten free oat streusel in the refrigerator while you prepare the gluten free muffin batter. You can also freeze the streusel 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. Step 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.

2. Step 2: Use an electric hand mixer to combine, or use a stand mixer fitted with the paddle attachment. Mix until light and fluffy.

3. Step 3: Transfer the cream cheese filling to a piping bag or zip-top bag. The easiest way is to place the bag tip-down inside a tall glass, fold the top edge over the rim to hold it open, spoon in the filling, then lift the bag out and twist the top closed.

4. Step 4: Set the cream cheese filling aside until the carrot cake muffins are ready to be assembled.

Gluten Free Carrot Cake Muffin Batter

This recipe for Gluten Free Carrot Cake Muffins comes together in no time, and the batter can be mixed by hand - no stand mixer or electric hand mixer needed. Just be sure to use a fine grater for the carrots.

1. Step 1: Peel and finely grate the carrots using the smallest setting on a box grater, then set them aside. I use about 3 medium carrots. Make sure to weigh them AFTER grating.
2. Step 2: In a small bowl, whisk or sift together the gluten free multi purpose flour, baking soda, baking powder, cinnamon, ginger, nutmeg, and kosher salt. Set aside.
3. Step 3: In a large mixing bowl, combine the oil (vegetable or canola works well), granulated sugar, brown sugar, room-temperature large eggs, and a generous teaspoon of vanilla extract until smooth and well combined.

4. Step 4: Whisk the wet ingredients together until fully combined.

5. Step 5: Add the dry ingredients to the wet ingredients and whisk together. You may need to switch to a flexible spatula if the batter becomes too thick to whisk.

6. Step 6: With a flexible spatula, fold the shredded carrots into the cake batter. Make sure they are evenly distributed.

Assembly & Baking Instructions

For tall, bakery-style gluten free muffins, line a 12-count muffin pan with 10 muffin liners. I prefer making my own muffin liners, which help the muffins rise higher, but if you're using standard liners, divide the batter evenly among all 12. Set the pan aside.

1. Step 1: Using a large cookie scoop (like this #20 scoop), evenly divide the gluten free carrot muffin batter between the muffin liners, filling each one all the way to the rim. 

2. Step 2: Next, grab your prepared cream cheese filling. Snip off the corner of the ziplock bag or the tip of the piping bag.
3. Step 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. Step 4: Top each muffin with a generous amount of oat streusel. Use your hands to gently press it on top of your muffin batter. At this point, you can refrigerate the carrot cheesecake muffins for up to 12 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. Step 6: Once the oven is fully preheated, bake the carrot 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 16-18 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. Step 7: Let the gluten free carrot cake muffins with cream cheese filling 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 enjoy these carrot cake muffins with cream cheese filling within a couple of days, store them in an airtight container at room temperature. This keeps the muffins soft, tender, and fresh.

If your kitchen runs warm, refrigeration is the better option. Place the muffins in an airtight container to prevent them from drying out. Stored this way, they’ll stay fresh for up to 3 days.

For longer storage, freezing works beautifully. Let the muffins cool completely, then arrange them on a sheet pan and freeze for 30 - 45 minutes, or until solid. Transfer the frozen muffins to an airtight container or freezer bag. They’ll keep well in the freezer for up to 2 months.

When ready to enjoy, thaw the muffins at room temperature or in the refrigerator overnight. For a quicker option, microwave for 15–30 seconds until soft and ready to eat.

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.