These yummy and Healthy Cinnamon Apple Muffins are a delicious way to make use of extra apples this apple season! Full of fresh apple chunks, and topped with a streusel topping and cream cheese glaze. They're naturally gluten-free and sugar-free made with almond flour and a sugar replacement.
You'll love this healthy apple muffin recipe. Full of wholesome ingredients, it's one of our favorite things to make in the fall. Enjoy them at breakfast or as an afternoon snack with a cup of coffee.
Looking for more apple recipes? You may also enjoy this sugar free apple cider, this instant pot apple butter, this sugar free apple crisp, this unsweetened applesauce, or this apple cinnamon oatmeal!
❤️Why we love this recipe
- Made with simple, healthy ingredients - You probably have most of the ingredients to make these muffins on hand in your kitchen and pantry already. Anything you don't already have can be picked up at almost any grocery store.
- No added sugar, naturally gluten free & low carb - This healthy apple muffins recipe is sweetened with a natural, zero-calorie, 1:1 sugar replacement, and the almond flour and gluten-free rolled oats make it naturally gluten-free! They're only 9 net carbs, and 3 grams of sugar per muffin.
- Perfect snack, dessert, or quick breakfast item - Don't you love a versatile treat? These muffins are delicious enough to be dessert, but healthy enough to be apart of breakfast or a snack.
Here are the ingredients we used for the muffins. You can find more information for substitutions below.
- Almond flour
- Gluten-free rolled oats - Check the package to make sure they are certified gluten-free, as many oats are produced in facilities with gluten. We love Bob's Red Mill (affiliate link).
- Baking powder & baking soda
- Xanthan gum - Since these muffins are gluten-free, xanthan gum helps improve the texture by keeping them from crumbling.
- Kosher salt
- Eggs & greek yogurt - Room temperature.
- Apple cider vinegar
- Vanilla extract or paste
- Unsalted butter
- Cream cheese - Softened.
- Brown sugar replacement - We use a 1:1 brown sugar replacement in this recipe, but this can easily be swapped for regular brown sugar, or white sugar.
- Powdered sugar replacement - We will need 1:1 powdered sugar replacement for the cream cheese glaze.
- Diced apples - Feel free to leave the peel on, as it adds color, texture, and flavor. You can also use grated apples, but we love the nice chunks of apple in our muffins. Use any kind of apple you prefer, we opted for sweet Honeycrisp apples.
Visit the recipe card for the full quantities and nutritional information.
✨Substitutions & variations
Here are a few simple swaps you can make to these muffins.
- Spiced - You can use apple pie spice in place of cinnamon if you prefer. You could also add more cinnamon for a stronger cinnamon flavor.
- Dairy free - To make this recipe dairy-free, you can use your favorite dairy-free yogurt, vegan butter in place of butter, vegan cream cheese in place of regular, and your favorite nut milk in place of regular milk.
- Swap the milk- You can make the glaze a little creamier by swapping it for heavy cream or half and half.
- Use a different sweetener - We love Swerve products (affiliate link) because they are a cup-for-cup sugar replacement! Feel free to use regular brown sugar and powdered sugar. You can also use coconut sugar in place of the brown sugar replacement.
- Omit the streusel topping or cream cheese glaze - Feel free to omit either component if you want a simpler muffin.
- Swap the vinegar - Feel free to use white vinegar instead of apple cider vinegar.
- Add pure maple syrup - For a little extra flavor, try adding some maple syrup (or sugar free maple syrup) to the cream cheese glaze.
- Use any kind of apples - You can use your favorite variety or a mixture of a few different types of apples. Granny smith apples are quite tart, while pink lady or gala apples will be quite sweet, so keep this
Unfortunately, this recipe hasn't been tested with any egg substitutes like flax eggs or different flours, so we can't provide any suggestions on how to substitute those at this time.
- Allow all dairy to sit out until softened. The cream cheese should be left out for at least 2 hours, preferably 4, before making the glaze. Eggs should sit out for about an hour, along with yogurt, milk, and if your apple cider vinegar is kept in the fridge, make sure that isn't cold either.
- Chop apples, and weigh ingredients using a kitchen scale. Having everything set out will make the process go very smoothly.
- Line a muffin tin with paper liners, and spray lightly with baking or cooking spray. This will prevent the muffins from sticking. Parchment paper liners (affiliate link) will also help prevent any sticking without the use of oil spray. Pro tip: We started leaving space between the muffins, meaning we only fill half of the muffin pan with liners and batter. This helps the muffins rise more! If you don't like paper liners, you can use silicone molds instead.
- Preheat the oven to 425°F.
Make the streusel topping. In a small bowl, combine melted butter, vanilla extract, brown sugar replacement, cinnamon, kosher salt, almond flour, and rolled oats. (Image 1).
Combine with a fork or your hands until a thick crumble texture is achieved (Image 2). Place the bowl in the freezer for the topping to firm up while you work on the muffin batter.
Make the muffin batter. In a large mixing bowl, cream together melted butter and brown sugar replacement with a hand mixer on medium speed. (Image 3).
Add in greek yogurt, vanilla extract, apple cider vinegar, and then eggs, one by one until completely mixed. (Image 4).
Add dry ingredients to the wet ingredients. Now, add in almond flour, rolled oats, cinnamon, kosher salt, baking powder, baking soda, and xanthan gum. (Image 5)
Mix dry ingredients until completely combined. (Image 6)
Add apple pieces. (Image 7) Then, with a rubber spatula, fold until combined. (Image 8)
Add to a muffin pan. Using a large cookie scoop, fill the muffin liners most of the way full, then sprinkle chilled streusel over the tops of the muffins. (Image 9)
Bake muffins. Add the muffins to a 425°F oven and bake for 5 minutes, then, without opening the oven door, drop the temperature to 350°F and bake for an additional 15-18 minutes, until a toothpick comes out mostly clean.
Allow the muffins to cool in the tin for 5 minutes (Image 10) then transfer them immediately to a wire rack to cool completely. (Image 11)
Make the cream cheese glaze. While the muffins are cooling, combine cream cheese, and softened butter in a medium bowl. Using a hand mixer, combine at medium speed until combined. Add in powdered sweetener, kosher salt, cinnamon, and vanilla paste, and mix again. (Image 12)
Add milk in a slow stream, mixing consistently until desired consistency is achieved. (Image 13)
Glaze and serve the muffins. Once muffins have cooled completely, drizzle with glaze, and enjoy! (Image 14)
- Weigh your ingredients using a kitchen scale. Measuring cups vary in size. Weighing ingredients will ensure you have the proper amount every time.
- Make sure your oven is at the right temperature before baking. Many ovens run hotter or cooler, so it's important to make sure it's at the right temperature before beginning.
- Use muffin liners! This ensures they will come right out of the pan. If you don't have muffin liners, be sure to grease the pan really well.
- Fill your liners up most of the way. These muffins don't rise as much as traditional muffins do, so you'll need to fill the muffin tin more.
- Bake fewer muffins at a time! Using two 12-muffin pans seems like an extra step, but allowing the muffins more room will encourage them to rise more.
- High heat to low heat creates the best muffins. Again, seems like an extra step, but the high heat allows the muffin tops to rise quickly. Dropping the temperature will prevent them from baking too much or burning, giving you the perfect muffin. Just make sure not to open the oven door!
- Always use room temperature ingredients. This ensures ingredients cream together properly.
- Don't let the muffins cool too long in the tin. These muffins do need an ample amount of time to cool and set up properly. Gluten free flours tend to be on the delicate side, due to the fact that they lack the gluten that all purpose flour has, so they just need longer to cool. With that being said, don't let them sit in the muffin tin after baking for much more than 5 minutes. This is because the muffins are so hot, and the tin traps the heat, making the bottoms too moist.
- Use fresh baking soda and baking powder. Since this recipe uses melted butter instead of softened butter, fresh baking powder, and baking soda are crucial to making the muffins rise! Both baking powder & soda should be replaced about every 30 days or so. To test if your baking soda is fresh, add about a teaspoon to a small bowl. Add in lemon juice or vinegar and if the mixture bubbles vigorously, it's good to go. For baking powder, add 1 teaspoon to a bowl with hot water. If it bubbles, it's fresh!
💭Frequently Asked Questions
Allow muffins to cool at room temperature on a wire rack until completely cooled. Store in an airtight container in the fridge once topped with cream cheese glaze for up to 5 days.
For longer storage, leave the cream cheese glaze separately from the muffins until it's time to serve.
Yes, to freeze, allow muffins to cool off completely at room temperature without the cream cheese glaze. Add to a baking sheet in a single layer, and freeze solid for about an hour and a half, then transfer to a freezer bag or container and freeze for up to 6 months.
To quickly get an egg to room temperature, you can place it in a bowl of lukewarm water for about 10 minutes.
Microwave cream cheese in a microwave-safe bowl at 50% power in 15-second increments until softened.
More Healthy Muffin Recipes To Consider
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Healthy Apple Cinnamon Muffins
- 224 grams almond flour (2 cups)
- 48 grams rolled oats (½ cup)
- 1 tablespoon ground cinnamon
- 2 teaspoons baking powder
- 1 teaspoon baking soda
- 1 teaspoon xanthan gum
- ½ teaspoon kosher salt
- 8 tablespoons unsalted butter, melted (1 stick)
- 192 grams brown sugar replacement (1 cup)
- 2 tablespoon apple cider vinegar
- 100 grams plain Greek yogurt, room temperature
- 1 tablespoon vanilla extract
- 3 large eggs, room temperature
- 1 large apple, cut into bite-sized pieces
Cream cheese glaze
- 2 ounces cream cheese, softened
- 2 tablespoons unsalted butter, softened
- 36 grams powdered sweetener (¼ cup)
- 1 teaspoon vanilla paste
- ½ teaspoon ground cinnamon
- ⅛ teaspoon kosher salt
- 5 tablespoons milk to thin (or more as needed)
- Preheat the oven to 425°F, and grease, and line a muffin tin with muffin liners. For a nice rise on the muffins, fill the muffin tin only halfway with liners and leave space between the muffins.
- Make the streusel topping. In a small bowl, combine melted butter, vanilla extract, brown sugar replacement, cinnamon, kosher salt, almond flour, and rolled oats. Combine with a fork or your hands until a thick crumble texture is achieved. Place the bowl in the freezer for the topping to firm up while you work on the muffin batter.
- Make the muffin batter. In a large mixing bowl, cream together melted butter and brown sugar replacement with a hand mixer on medium speed. Add in greek yogurt, vanilla extract, apple cider vinegar, and then eggs, one by one until completely mixed.
- Add dry ingredients to the wet ingredients. Now, add in almond flour, rolled oats, cinnamon, kosher salt, baking powder, baking soda, and xanthan gum. Mix dry ingredients until completely combined. Add apple pieces, then, with a rubber spatula, fold until combined.
- Add to a muffin pan. Using a large cookie scoop, fill the muffin liners most of the way full, then sprinkle chilled streusel over the tops of the muffins.
- Bake muffins. Add the muffins to a 425°F oven and bake for 5 minutes, then, without opening the oven door, drop the temperature to 350°F and bake for an additional 15-18 minutes, until a toothpick comes out mostly clean. Allow the muffins to cool in the tin for 5 minutes, then transfer them immediately to a wire rack to cool completely.
- Make the cream cheese glaze. While the muffins are cooling, combine cream cheese, and softened butter in a medium bowl. Using a hand mixer, combine at medium speed until combined. Add in powdered sweetener, kosher salt, cinnamon, and vanilla paste, and mix again. Add milk in a slow stream, mixing consistently until desired consistency is achieved.
- Glaze and serve the muffins. Once muffins have cooled completely, drizzle with glaze, and enjoy!
- Store in an airtight container in the fridge for up to 5 days. You can store it at room temperature in an airtight container for up to 3 days if the glaze is left off until just before serving. To freeze, add to a baking sheet after they have cooled off completely and freeze solid. Transfer to a freezer-safe bag or container, and store for up to 6 months. Leave the glaze off if freezing.
- Weigh your ingredients using a kitchen scale to ensure your measurements are correct every time.
- Make sure your oven is at the right temperature before baking, as oven temperatures can vary.
- Use muffin liners so the muffins don't stick.
- Fill your liners up most of the way, as these muffins don't rise much.
- Bake fewer muffins at a time, and use the high-to-lower heat method for the best round-shaped tops on the muffins.
- Always use room temperature ingredients.
- Don't let the muffins cool too long in the tin, or they will become soggy.
- Use fresh baking soda and baking powder.