These light and fluffy Paleo Apple Cinnamon Muffins are chock-full of fall flavors! 

paleo apple cinnamon muffins on a marble board surrounded by apples

Once the last warm days of summer give way to the crisper weather of fall, we start to crave classic autumnal flavors like apples and warming spices such as cinnamon, ginger, and cloves. There’s nothing like those first cool days of the season when you get inspired to bake something up that makes the entire house smell of fragrant fall fruit and baking spices.  

That’s where these Paleo apple cinnamon muffins come in. These muffins showcase all those cozy fall flavors, are easy to make (you don’t even have to pull out your mixer), smell amazing while they bake, and result in a perfectly moist, lightly sweet muffin that is perfect for breakfast or brunch.

Enjoy them on their own as a healthy breakfast or snack, or eat them alongside Quiche Lorraine, Healthy Breakfast Salad, Egg Muffin Cups, or our Blueberry Sweet Potato Breakfast Meatballs for a heartier brekkie or brunch.

Why You’ll Love This Recipe

  • A delicious medley of fall flavors: apples, cinnamon, ginger, and cloves 
  • Only 15 minutes of prep, and ready in 35 total
  • Makes a big batch of 18 muffins: enough to eat some now, and freeze some for later

Apple Cinnamon Muffins Recipe Ingredients

Here’s everything you’ll need to make the two components of these muffins: the batter and the crumble. Find ingredient notes (including substitutions and swaps) below.

Ingredients for paleo apple cinnamon muffins sit in a variety of bowls and plates on a light grey surface.

For the Muffins

  • Flour – 3 cups 278 g paleo baking flour
  • Sugar – 1 1/2 cups coconut sugar
  • Baking powder – 1 tablespoon plus 1 teaspoon baking powder
  • Baking soda – 1/2 teaspoon baking soda
  • Cinnamon – 1 tablespoon cinnamon
  • Ginger – 1 1/2 teaspoons ground ginger
  • Nutmeg – 1 teaspoon nutmeg
  • Cloves – 1/2 teaspoon ground cloves
  • Salt – 1/4 teaspoon coarse salt
  • Eggs – 4 eggs
  • Butter – 1 cup butter melted (may also use ghee or coconut oil)
  • Vanilla – 2 teaspoons vanilla extract
  • Apples – 2 apples grated, about 1 cup total

For the Crumble

A full ingredient list with exact amounts can be found in the recipe card below.

Recipe Variations and Modifications

Here are a few simple ways to make this recipe your own:

  • Nuts – if you’d prefer, feel free to swap the pecans for another nut, like almonds, hazelnuts, or walnuts
  • Spices – this recipe calls for cinnamon, ginger, nutmeg, and cloves. But if you don’t have all of these spices on hand, don’t fret! You can either double up on one of the other spices, or use the same amount of pumpkin pie spice, which is a blend of all these spices.

How to Make Apple Cinnamon Muffins

Now, let’s jump into how to make these delicious apple muffins!

Ground cinnamon is tossed into a stainless steel bowl on a light grey surface.
An egg and butter mixture is whisked in a stainless steel bowl on a light grey surface.

Step 1: The first thing you’ll do for this recipe is to whisk together the flour, coconut sugar, baking powder, and spices. Once the mixture is fully incorporated, set it aside.

Step 2: Next, you’ll whisk together the eggs, vanilla, and butter or ghee in a separate bowl, until fully blended.

Grated apple sits on top of a paleo cinnamon muffin batter in a stainless steel bowl on a light grey surface.
A crumble mixture sits in a stainless steel bowl on a light gray surface.

Step 3: Now you’ll stir the dry ingredients into the wet ingredients until the batter is fully combined. The batter will be slightly stickier and wetter than a traditional batter. Once the batter is formed, you’ll stir the grated apple into it until it is evenly distributed.

Step 4: For the crumble topping, you’ll add the butter, sugar, and coconut flour to a small bowl and work the mixture with your hands until it is fully combined. It will be more of a paste-like consistency than a traditional crumble.

Paleo apple cinnamon muffin batter topped with a crumble mixture and pecans batter sits in white liners in a 12 muffin tin on a light grey surface.

Step 5: Finally, you’ll fill your muffin tins about 3/4 of the way full, take a bit of the crumble and flatten it with your hands to make enough to cover the muffin, place it on top of the muffin, sprinkle on pecans, and bake for 17-20 minutes, until a toothpick inserted into the center of the muffin comes out clean. Let the muffins cool slightly, then enjoy!

Recipe Tips

Freeze for later – this recipe makes a big batch of 18 muffins that freeze well. If you want to save some for later, place them in a single layer on a baking sheet until they’ve firmed up. Then, wrap them individually and place them in a large freezer bag.They’ll keep for up to 3 months.

Slather with spreads – while these muffins are delicious on their own, you can also eat them with spreads like butter or nut butters like almond, hazelnut, or cashew.

How to Serve Cinnamon Apple Muffins

Serve these lil’ babies warm from the oven, or at room temperature plain — or with butter or nut butter.

How to Store and Reheat Muffins

These cinnamon apple muffins will keep for up to 5 days, so they are perfect to make over the weekend and eat for breakfast during the week! For the best texture, we recommend storing your muffins in the refrigerator then quickly microwaving or toasting them before eating.

an apple cinnamon muffin cut in half with butter on top surrounded by more muffins all on a marble countertop

Frequently Asked Questions

Can these muffins be made egg-free?

They can! In fact, we tested a TON of different egg substitutes in several different baked goods, took all kinds of notes, and then laid it all out for you in this super helpful guide to egg-free baking. For muffins (though this isn’t a Paleo option), we recommend subbing in plain Greek yogurt (¼ cup of yogurt per egg) – Greek yogurt made for fluffy and slightly crisp on the outside muffins that had a really delicious flavor and held together really well.

If you tried this recipe for Paleo Apple Cinnamon Muffins, or any other recipe on the Fed & Fit website, please leave a 🌟 star rating and let us know how it went in the 📝 comments below!

Paleo Apple Cinnamon Muffins

5 — Votes 2 votes
By Amber Goulden
Prep: 15 minutes
Cook: 20 minutes
Total: 35 minutes
Servings: 18 muffins
These Paleo apple cinnamon muffins are moist, fluffy, and filled with apple flavor!

Ingredients  

For the Muffins

For the Crumble

Instructions 

  • Preheat the oven to 350 F and line a muffin tin with parchment paper liners.
  • Add the flour, coconut sugar, baking powder, baking soda, cinnamon, ginger, nutmeg, cloves, and salt to a medium-sized bowl and whisk to combine, smoothing out any lumps.
  • In a large bowl, beat the eggs, melted butter, and vanilla extract. Then, mix the dry ingredients into the wet and whisk until fully combined. Stir the grated apple into the batter until evenly distributed Spoon the batter into the muffin tins until they are almost all of the way full.
  • To make the crumble, combine the softened butter, coconut sugar, and coconut flour in a small bowl and work the mixture with your hands until it takes on a paste-like consistency.
  • Flatten the crumble mixture with your hands to make enough to cover a muffin, and place it on top of the muffin batter. Repeat for each muffin.
  • Sprinkle the pecans over top of the muffins, then bake for 18-20 minutes, until a toothpick inserted into the center of the muffin comes out clean. Let cool then enjoy!

Nutrition

Calories: 341kcal | Carbohydrates: 24g | Protein: 6g | Fat: 27g | Saturated Fat: 11g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 1g | Cholesterol: 77mg | Sodium: 306mg | Potassium: 52mg | Fiber: 3g | Sugar: 15g | Vitamin A: 539IU | Vitamin C: 1mg | Calcium: 96mg | Iron: 1mg

Additional Info

Course: Breakfast
Cuisine: American
Servings: 18 muffins
Calories: 341
Keyword: almond flour, grain free, paleo

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Elizabeth Brownfield


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8 Comments

  1. Hello Cassy and Fed+Fit Team,
    Do you have any thoughts regarding glyphosate found in non-organic flours made with almonds? You can also just link to research you have done to form your opinion. I have mostly avoided almond flour because of what I have read. I have your book and I frequent your website so I trust your research. Thanks in advance for your time!

  2. 5 stars
    Oh my, these are THE best paleo muffins I have ever made! I did not make the crumble topping instead topped with candies pecans. They are very flavorful and sweet. The texture is fluffy and moist, not at all the usual dense heavy paleo texture. Thank You fed and fit team, I will make these again

    1. Wahoo!! So glad you loved these, Ashley! Thank you for sharing this with us!

  3. 5 stars
    Cassy and Fed & Fit team, I made these apple muffins yesterday morning and they are the bomb. I used ingredients I had at home (almond flour, fresh ginger) and both my husband and myself loved them. Gracias mil!

  4. This flour really has me interested. I would like to bake with different flours, however, I havenโ€™t had good results. Iโ€™ve baked with white wheat and wheat pastry flour and the end product has a chalky thick taste. I am going to look for this next time Iโ€™m shopping. Recipe sounds yummy!