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These soft and fluffy Gluten-Free Pumpkin Muffins are made with a blend of almond and coconut flour, maple syrup, pumpkin, and spices. They’re only 146 calories, with 6 grams of protein, and over 3 grams of fiber.

Quick Summary: Gluten-Free Pumpkin Muffins
- Why Make This Recipe: These almond flour pumpkin muffins are the ideal healthy alternative to fall treats. They are fluffy and full of fall flavor with less sugar and calories.
- Nutrition: 146 calories, 6 grams of protein, 3.5 grams of fiber
- Diet: Low-Calorie, Paleo, Gluten-Free, Dairy-Free
- Time: 10 minutes of prep time, 25 minutes of cook time, 35 minutes total
- Method: Baked
- Best for: Grab a muffin for breakfast on a busy fall morning, or cozy up with a coffee and enjoy one as a sweet treat later in the day.
- Tip: Use room-temperature eggs to help your muffins rise more.
All of your favorite fall flavors, like pumpkin, cinnamon, cardamom, nutmeg, ginger, and cloves, infuse each bite of these almond flour pumpkin muffins. They’re a spinoff of my almond flour banana bread muffin recipe, only with pumpkin. They’re lightly sweetened with maple syrup, so they’re not overly sweet. I find if things are too sweet, I want to eat the whole batch!Â
The almond flour contains more protein and fiber than a typical gluten-free flour blend, so I love using it in my baked goods. Those are the ingredients that will satisfy your hunger and keep you feeling satisfied. I love to batch these muffins so I can eat them throughout the week as part of my breakfast, a post-gym snack, or dessert.
If you like healthy muffin recipes, you will love my butternut squash chocolate chip muffins and chickpea chocolate chip muffins!
Why You’ll Love This Recipe
- Fluffy, Not Crumbly: Almond flour makes muffins rich and tender, but since there’s no gluten to hold things together, it can turn out a little crumbly on its own. Adding a few tablespoons of coconut flour solves this issue. It’s high in fiber and soaks up liquid, so it gives the batter more body and helps the muffins hold their shape.
- Naturally Gluten-Free and Dairy-Free: Almond flour and coconut flour are naturally gluten-free, plus this muffin recipe doesn’t contain any milk, making it dairy-free as well.
- Healthy Alternative to Fall Treats: With only 146 calories, plus the protein and fiber, these Paleo pumpkin muffins are the perfect low-calorie treat. Thanks to the pumpkin and spices, they taste just as good as a bakery muffin.
Table of Contents
Ingredients

- Pumpkin Puree: Be sure to use a 100% pumpkin puree, not pumpkin pie filling. The pie filling is full of sugar and other spices.
- Almond Flour: This gluten-free flour is nutrient-dense, low-carb, and has a low glycemic index. It’s also great for your digestive health. Be sure to use finely ground flour, not almond meal.
- Coconut Flour: This flour is loaded with fiber and also has a lower glycemic index, which makes it a great flour alternative.
- Eggs: Use room temperature eggs to give your muffins structure and help them rise.Â
- Fall Spices: These muffins are packed with cinnamon, nutmeg, ginger, cloves, and cardamom to maximize the fall flavors.
- Chocolate Chips: Add dairy-free chocolate chips for a little chocolate treat inside your muffins. If you don’t need this recipe to be dairy-free, you can use regular chocolate chips.
See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.
Variations & Dietary Modifications
- Add Nuts: Give your muffins a little extra crunch and add chopped pecans or walnuts to the batter.Â
- Mix In Fruit: Pumpkin and berries taste great together, so try mixing some blueberries or blackberries into the batter. You could also try adding apples, like in my pumpkin apple crumble.
- Make Them Mini: Use a mini muffin tin to turn these into bite-sized treats. Bake in a greased mini muffin tin at 350°F for 10–14 minutes, or until a toothpick inserted in the center comes out with just a few loose crumbs.
How to Make Gluten-Free Pumpkin Muffins
If you love all things pumpkin in the fall, you need to make these low-calorie pumpkin muffins! They are bursting with flavor and only take 35 minutes to make. Be sure to preheat your oven to 350°F and line your muffin tin with liners or grease the cavities with cooking spray before you get started.

- Step 1: Mix Dry Ingredients. Sift together the almond flour and coconut flour in a large mixing bowl. Add the baking soda, cinnamon, nutmeg, ginger, cloves, cardamom, and salt.

- Step 2: Combine Wet Ingredients. In a separate mixing bowl, beat together the eggs, pumpkin puree, maple syrup, vanilla extract, and oil with a hand mixer until the ingredients are smooth.

- Step 3: Combine Wet and Dry Ingredients. Add the dry ingredients to the wet and mix them until the batter is smooth. Do not overmix the batter.

- Step 4: Fill Muffin Cavities. Transfer the batter into the prepped muffin tin. It will divide evenly among 10 cavities. Then, add chocolate chips to the tops of the muffins and gently press them in using your fingers.

- Step 5: Bake. Place the tin in the oven and bake the muffins at 350°F for 25 minutes, or until a toothpick can be inserted and removed cleanly from the center. Let the muffins cool on a wire baking rack for 10 minutes before eating them. Enjoy with a savory breakfast loaded with protein, like this tomato egg casserole with sausage.
Expert Tips
- Use Room Temperature Eggs: It’s important to use room temperature eggs for baking because they blend more smoothly into the batter and help trap air for a fluffier texture.
- Measure the Flour Properly: When baking with gluten-free flours, it’s especially important to properly measure the flour. If you scoop it directly with a measuring cup, you may use too much flour and make your muffins dry and dense.Â
- Makes 10 Muffins: Keep in mind that this recipe yields 10 muffins, not 12! Don’t underfill your muffin cavities trying to make a dozen muffins.
- Storing: Keep leftover muffins in an airtight container on the counter for 2 days or in the refrigerator for 7 days. You can also wrap each muffin individually and freeze them for up to 3 months.

Serving Suggestions
Nothing beats a warm muffin, especially on a crisp fall day. These dairy-free pumpkin muffins with spices are the perfect addition to your fall meal prep. Whether you want to enjoy them after the gym or as part of your breakfast, they’ll be on hand for you to grab and enjoy.
- Enjoy a cozy fall breakfast of pumpkin muffins, a healthy breakfast hash with butternut squash, and a low-cal pumpkin spice latte on the weekend.
- After the gym, grab a pumpkin muffin and a pumpkin protein smoothie to fuel your body while also enjoying a treat.
Gluten-Free Pumpkin Muffins Recipe FAQs
No, other gluten-free flours will not work the same as the almond flour in this recipe. If you are looking for a nut-free pumpkin muffin, try my pumpkin oatmeal muffin recipe instead.Â
There are a few reasons why your muffins turned out dense and gummy. One reason is if the batter was overmixed. Be sure to stop mixing once everything is well combined. Using cold eggs or too much flour will also create this problem as well. Be sure to use room temperature eggs and measure the flour by spooning it into the measuring cup instead of scooping it.Â
No, you cannot make this recipe without eggs. They are necessary for providing structure for the muffins.Â

More Delicious Pumpkin Breakfast Recipes
If you tried this Gluten-Free Pumpkin Muffins recipe or any other recipe on my website, please leave a 🌟 star rating and let me know how you go in the 📝 comments below.
















I love working out in the morning, I feel like my motivation is always highest then. I teach early morning classes and it can be pretty hit or miss sometimes. I think especially on Mondays, when folks have been sleeping in over the weekend, it makes it harder to get up. It is weird to teach really small classes sometimes, but I am sure they really appreciate you being there.
I’m with you on the early morning classes and it is true that the people who do show up probably appreciate it a lot. 🙂
I used to workout that earlier. I can’t anymore, but I’ll still gladly eat these muffins for breakfast!
I will send you some! <3
You know what’s funny? I used to HAVE to get a workout in the morning or it just wouldn’t happen. For years I worked out VERY FIRST thing in the morning. Then, fitness became a part of my lifestyle and I started testing afternoon workouts, or late mid-morning (because sometimes my schedule allows it now). I found I got a better workout because I was a little more awake and had some fuel in me. I still workout first thing in the morning sometimes now, but I’m okay to schedule them in and get them in later too. But that took 5 years of consistent working out.
I can’t workout later in the day anymore. With my Hashimoto’s my energy and fatigue is very high in the afternoon and evenings. When I have to sub cycle classes in the evenings I have to take a nap and even then it’s tough for me to get through. So different for everyone!
I so wish my gym had a 5:15am spin class! The 6:15 is just too late for me to get to work on time. I hope one day to try one of your classes if I’m in the area!
I would think most people would want an earlier class, but maybe it’s just hard getting up that early on a Monday. I would love to have you come!