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These healthy Apple Cinnamon Muffins are made with almond flour, coconut flour, egg whites, freshly diced apple, and warm cinnamon, delivering all your favorite fall flavors. They’re naturally gluten-free and dairy-free, about 272 calories each with 8 grams of protein and 5 grams of fiber.

Quick Summary: Apple Cinnamon Muffins
- Why Make This Recipe: These fluffy apple cinnamon muffins are full of fresh apple and apple pie flavor. They make the perfect portion-controlled fall snack or dessert.
- Nutrition: 272 calories, 8 grams of protein, 5 grams of fiber
- Diet: Low-Calorie, Gluten-Free, Dairy-Free, Paleo
- Time: Prep Time = 10 minutes, Bake Time = 30 minutes, Total Time = 40 minutes
- Method: Baked
- Best for: A delicious breakfast or snack on the go that’s easy to make ahead and freeze.
- Tip: The batter for these muffins should be thick because it helps the apples not sink to the bottom.Â
These low-calorie apple muffins with almond flour are the perfect replacement for bakery muffins. They are moist and bursting with flavor, but have a fraction of the sugar and calories.
\Many bakery muffins have 300-400 calories, whereas these only have 272 calories and are sweetened with just 2 tablespoons of honey. Plus, these muffins have protein and fiber to help you feel satisfied and to fuel your day.
If you like easy apple breakfast recipes, you will love my healthy apple pancakes and apple and Brussels sprouts breakfast hash.
Why You’ll Love This Recipe
- Packed with Protein: Almond flour has more protein than regular flour, so paired with the egg whites, it packs 8 grams of protein into each muffin.
- One Whisk, Two Bowls, No Mixer: There’s no need for stand mixers or electric mixers with these muffins. The batter comes together in two bowls using a whisk and then a spoon.
- Freezer-Friendly: Store your muffins in the freezer for up to 3 months for a perfectly portioned breakfast or snack anytime.Â
Table of Contents
Ingredients

- Apples: Use firm, sweet-tart apples such as Honeycrisp, Pink Lady, Gala, or Granny Smith apples because they will keep their shape and the flavor stands out.
- Egg Whites: Use room-temperature egg whites, which are full of protein but contain less fat and calories than whole eggs.Â
- Honey: These muffins are naturally sweetened with honey, but you can use maple syrup instead.Â
- Almond Flour: Almond flour is high in natural fats and oils to make the muffins more moist. It also contains protein and fiber.Â
- Coconut Flour: Coconut flour is very absorbent, which helps balance the excess fats and oils in almond flour. It is also packed with fiber.
See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.
Variations & Dietary Modifications
- Add Nuts, Berries, or Veggies: Give your muffins a little crunch by mixing in chopped walnuts or pecans. You could also add blueberries, raisins, or even veggies, like in my apple and carrot muffins.
- Swap for Pears: Apples are a popular fruit for fall, but pears are just as delicious!Â
- More Spices: This recipe just calls for cinnamon, but you can bring out more robust fall flavors by also adding nutmeg and cloves or a prepackaged apple pie spice.
- Use Whole Eggs: Instead of egg whites, you can use whole eggs for these muffins. Just keep in mind that this will change the calories and fat content.
How to Make Apple Cinnamon Muffins
There’s just something comforting about a warm, cinnamon-packed muffin bursting with natural sweetness and nutty goodness. They come together without an electric mixer, just a whisk, a spoon, and two bowls. You’ll also need to preheat your oven to 350°F and use muffin liners or grease your muffin tin with cooking spray.

- Step 1: Mix Dry Ingredients. Combine the almond flour, coconut flour, baking soda, cinnamon, and salt in a medium bowl using a whisk.Â

- Step 2: Whisk Wet Ingredients. In a separate bowl, whisk together the egg whites, honey, and olive oil.

- Step 3: Combine Wet and Dry. Fold the dry ingredients into the wet ingredients and stir until they are just combined. Then add the chopped apples.

- Step 4: Scoop and Bake. Scoop the batter into the muffin tins until they are ¾ full. Use your finger to smooth the edges of the muffins. Bake them for 22-25 minutes at 350°F until they are golden brown. Then remove from the oven and let cool for 5-10 minutes before transferring to a wire rack to cool completely.
Expert Tips
- Thick, Scoopable Batter: This batter is very thick and easy to scoop. It’s ideal because it prevents the apple chunks from sinking to the bottom of the muffins.
- Measure Flour Properly: It’s important to properly measure the flour when baking with gluten-free flour. Scooping it directly with a measuring cup may cause you to use too much flour, which will make your muffins dry and dense.Â
- Create a Dome: Create the perfect round dome on the top of the muffins by running your finger around the edge of the muffin liner. This slightly pushes the batter to the middle of the muffin.
- Storing: Keep muffins in an airtight container on the counter for 1-2 days, or in the refrigerator for 5 days. You can freeze the paleo apple muffins for up to 3 months.

Serving Suggestions
If you love apple desserts, like apple pie or apple crisp, you’ll love these gluten-free apple muffins! They are bursting with cinnamon and fresh apple chunks, but are also full of fiber and protein to help keep you feeling satisfied. They make a great dessert or breakfast for Thanksgiving, but you can enjoy them all year round as well.Â
- Balance a sweet and savory breakfast and serve these low-calorie apple muffins with a crockpot eggs omelet.
- Use any leftover apples to make a light apple walnut salad for lunch and enjoy a muffin for dessert.
- Add more protein to your afternoon or post-workout snack and enjoy a muffin with an apple smoothie or a cranberry apple smoothie.
Apple Cinnamon Muffins Recipe FAQs
No, you don’t need to peel the apples. The apple skins are loaded with fiber, so it’s best to leave them on.
No, applesauce cannot be used as a substitute because it adds too much moisture to the batter, and the flour measurements don’t accommodate it.Â
No. This recipe was made for almond and coconut flour, and other gluten-free flours will not work with it as is. If you’d rather make apple muffins with oat flour, try my healthy apple muffins with oats recipe instead.

More Healthy Apple Dessert Recipes
If you tried this Apple Cinnamon 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.
















These look fabulous! I love almond meal baked goods. Such a fabulous texture!
Thank you! Hope you get to try them.
Oh yum! I bet the house smells amazing while these bake!
And I agree — actions speak louder than words. I’d devour these (that’s an action, right)?! 🙂
Glad to see another delicious muffin recipe back on the blog!
That’s a good action! Muffins have been a little MIA lately. I need to get on them.
YUMMMMMMMMMMMMMMMMMMMMMMM
Thank you!
These sound delish and super easy! Making them soon! =)
Awesome, hope you like them!