Spice Up Your Fall Menu With These Easy-Bake Healthy Cinnamon Apple Muffins

Naturally sweetened, grain-free, and paleo.

By: Lexy Parsons

Step aside pumpkins! Apple and cinnamon deserve their time in the seasonal spotlight. And, what better way to debut their deliciousness than in the form of healthy baked goods? If you’ve been searching for nourishing autumn treats, look no further. These Healthy Cinnamon Apple Muffins make the perfect grab-and-go breakfast for busy mornings, a yummy mid-day snack, and even a nourishing late-night treat when you’re craving something healthy but sweet. You can even serve them up at your next holiday gathering! Best of all, they’re grain-free, paleo-friendly, and made with nourishing ingredients like almonds, pecans, and warming cinnamon spice.

And, as an added bonus, these healthy cinnamon apple muffins will have your entire house smelling like an apple-spiced bakery.

Healthy Cinnamon Apple Muffins Ingredients


This sweet, seasonal fruit is not only reminiscent of fall, but it’s just as healthy as it is tasty. We added apples to these Healthy Cinnamon Apple Muffins for an all-natural sweetener, plus they’re full of nutrients like antioxidants, vitamin C, and fiber to aid digestion.

Almond Flour 

To make this recipe grain-free and paleo-friendly, we used almond flour in place of oats or whole wheat flour. Almond flour is light, fluffy, and incredibly nutritious. It’s rich in vitamin E, magnesium, and it contains more protein, fat, and fiber than its whole wheat cousin (but fewer carbs!)


We used eggs as a protein-packed binding ingredient in this recipe. They’re a nutritional powerhouse and could even aid weight loss when eaten for breakfast! A single egg contains 6 grams of complete protein, all essential amino acids, B vitamins, minerals, and a rich antioxidant profile. Impressive, we know! So, we added 4 to this recipe. 

If eggs don’t fit in your lifestyle, you can still make these healthy cinnamon apple muffins! Simply sub an equal number of flax or chia eggs for whole eggs.

Coconut Oil 

Coconut oil is a healthy alternative to heavily processed oils like vegetable oil or canola oil. It’s high in anti-inflammatory ingredients, contains rich fatty acids that promote satiety, and has a slightly sweet coconut flavor profile that complements the warming fall spices in this recipe. 

Maple Syrup

For a yummy sweetener made with everything you’ll love (and nothing you won’t), we turned to Maple syrup. Unlike table sugar and other artificial flavors, this unrefined sweetener carries an impressive nutrient profile. For starters, maple syrup contains vitamins and minerals like zinc and manganese and is rich in antioxidants.


Full of antioxidants (containing the highest flavonoid content of all nuts) and plant-based protein, we couldn’t skip this sweet and creamy fall flavor!

Lemon Juice

We added a splash of lemon juice for a bright, citrusy element of freshness. Lemons enhance the flavor without adding calories or sugar, plus they boost digestion and contain high levels of vitamin C.

Spices & Toppings 

We couldn’t make cinnamon-spiced muffins without the cinnamon! This fall-flavored spice is not only sweet and flavorful, but it’s full of antioxidants and anti-inflammatory properties. 

To finish, we swapped the butter and cream cheese for a healthier topping alternative: protein-packed almond butter! It pairs perfectly with fall flavors and helps increase satiety (thanks to its protein and fat content). Pecan butter, walnut butter, sunflower seed butter, and Greek or coconut yogurt make delicious toppings too! 

Cinnamon Apple Muffins


  • 3 cups almond flour
  • 1 tbsp cinnamon
  • 1 pinch salt
  • 3 tsp baking powder
  • 4 eggs
  • ¼ cup coconut oil, melted
  • 3 tbsp maple syrup
  • 1 apple, chopped or grated
  • ½ cup pecans, roughly chopped
  • ½ lemon, juiced 
  • 1 tbsp coconut sugar 
  • Dollop of almond butter for serving 

Step #1: Preheat the Oven & Gather Your Ingredients 

Start by preheating your oven to 320°F. While the oven is heating, gather your ingredients and line a muffin tin with muffin liners.  

Step #2: Add Your Dry Ingredients to a Bowl 

Next, add the almond flour, cinnamon, salt, and baking powder to a large mixing bowl and stir to combine. 

Step #3: Prep Your Wet Ingredients

Crack the eggs into a separate mixing bowl and whisk. Add the melted coconut oil, maple syrup, and vanilla. 

Step #4: Combine the Wet and Dry Ingredients to Form a Batter

Add the wet mixture into the bowl with the dry ingredients and mix well. Next, fold in the grated apple, lemon juice, and pecans. Stir until well combined!

Step #5: Pour the Batter into the Muffin Tins & Add Any Toppings

Pour the batter into the lined muffin tins and top with extra pecans and a sprinkle of coconut sugar. 

Step #6: Bake until Golden Brown

Bake for 25-30 minutes until the muffins are golden and cooked through. 

Step #7: Remove from the Oven, Add Any Toppings & Serve! 

Once the muffins are ready, serve them with a dollop of almond butter. Enjoy! 

A Sweet Way to Spice Up Your Fall

These nutritious cinnamon apple muffins will have you falling in love with every seasonal bite. Best of all, they can be easily modified for any eating preference! Swap the eggs and make them plant-based, go nut-free by trading pecans and almond butter for seeds like sunflower or pumpkin, or up the protein content by serving them with a dollop of Greek yogurt or an extra serving of almond butter. 

This simple recipe proves fall baking can be healthy, simple, and oh so sweet! For more yummy recipes to fuel your fall, sign up for FitOn PRO and get access to delicious recipes and personalized meal plans.