Irresistible Apple Pumpkin Breakfast Muffins

Finding time to make a nutritious breakfast that actually tastes good can feel impossible when you’re rushing around on busy mornings. Between getting everyone ready for school and work, it’s tempting to just grab whatever’s quickest, even if it’s not the healthiest choice.

That’s where these apple pumpkin breakfast muffins come to the rescue. They’re packed with good-for-you ingredients, taste like fall in every bite, and can be made ahead of time so you can just grab one and go. Plus, they’re sweet enough that even picky eaters will happily munch on them.

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What Kind of Apple Should I Use?

For these breakfast muffins, you’ll want to pick an apple that holds its shape well when baked and won’t turn to mush. Granny Smith apples are a great choice because they’re tart and firm, which balances nicely with the sweetness from the brown sugar and dried cranberries. Honeycrisp or Gala apples also work well if you prefer something a bit sweeter. When you’re shredding your apple, you can leave the peel on for extra fiber and nutrition – just make sure to wash it thoroughly first. The key is to shred it right before adding it to your batter so it doesn’t brown too much.

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Options for Substitutions

These muffins are pretty forgiving when it comes to swapping ingredients, so here are some easy substitutions:

• Whole wheat flour: You can use all-purpose flour instead of whole wheat, but your muffins will be a bit lighter in texture and flavor. For a gluten-free option, try a 1:1 gluten-free flour blend.
• Coconut oil: If you don’t have coconut oil, melted butter or vegetable oil work just fine. You can also use additional applesauce (up to 1/2 cup total) for a lower-fat version.
• Pumpkin puree: Sweet potato puree or butternut squash puree make great substitutes. You could even use mashed banana, though it will change the flavor profile a bit.
• Dried cranberries: Swap these with raisins, dried blueberries, or mini chocolate chips if that’s what you have on hand.
• Pecans: Walnuts, almonds, or pumpkin seeds all work well here. You can also leave the nuts out completely if you have allergies.
• Pumpkin spice: Make your own by mixing 1 teaspoon cinnamon, 1/2 teaspoon ginger, 1/4 teaspoon nutmeg, and 1/4 teaspoon allspice.
• Flaked coconut: This can be left out entirely or replaced with extra nuts or dried fruit if you’re not a coconut fan.

Watch Out for These Mistakes While Baking

The biggest mistake you can make with these muffins is overmixing the batter, which leads to tough, dense muffins instead of light and fluffy ones – mix just until the dry ingredients are barely combined with the wet ingredients, even if you see a few lumps.

Another common error is using pumpkin pie filling instead of pure pumpkin puree, which contains added spices and sugar that will throw off the flavor balance and texture of your muffins.

Make sure your coconut oil is melted but not hot when you add it to the mixture, as hot oil can start cooking the other ingredients and create an uneven texture.

To prevent your add-ins like cranberries and pecans from sinking to the bottom, lightly coat them in flour before folding them into the batter, and don’t forget to fill your muffin cups only about 2/3 full to avoid overflow during baking.

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What to Serve With Apple Pumpkin Breakfast Muffins?

These muffins are packed with so much good stuff that they’re practically a meal on their own, but I love pairing them with a hot cup of coffee or chai tea to bring out those warm spices. A dollop of Greek yogurt on the side adds some extra protein and creamy texture that complements the muffins perfectly. If you want to make it feel more like a complete breakfast spread, try serving them alongside some scrambled eggs or a fruit salad with seasonal apples and pears. For a cozy weekend brunch, I sometimes warm them up slightly and serve with a light drizzle of honey or a pat of butter.

Storage Instructions

Keep Fresh: These muffins stay moist and delicious when stored in an airtight container at room temperature for up to 4 days. The apple and pumpkin keep them nice and tender, so they don’t dry out as quickly as regular muffins. I like to grab one for breakfast on busy mornings!

Freeze: Apple pumpkin muffins freeze really well for up to 3 months. Wrap each muffin individually in plastic wrap or store them in a freezer-safe container with parchment paper between layers. This way you can pull out just one or two whenever you want a quick breakfast.

Warm Up: To enjoy frozen muffins, just thaw them at room temperature for about 30 minutes, or pop them in the microwave for 20-30 seconds. If you want them extra cozy, warm them in a 300°F oven for 5-7 minutes. They taste almost as good as fresh from the oven!

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 2500-2700
• Protein: 28-34 g
• Fat: 105-115 g
• Carbohydrates: 390-420 g

Ingredients

• 1 1/2 cups whole wheat flour
• 1/2 cup plain flour
• 3/4 cup packed light brown sugar
• 1 tbsp baking powder
• 2 tsp baking soda
• 2 tsp pumpkin pie spice
• 1/2 tsp ground cinnamon
• 1/2 tsp salt
• 3/4 cup pure pumpkin (not pie filling)
• 1/4 cup unsweetened applesauce
• 1/2 cup melted coconut oil
• 1 large apple, coarsely grated
• 1 tbsp vanilla extract
• 2 cups grated carrots (from about 3 medium carrots)
• 1/2 cup dried cranberries
• 1/2 cup shredded coconut
• 1/2 cup chopped pecans

Step 1: Prepare the Muffin Tin and Oven

Line a 12-mold muffin tin with paper liners and set aside.

Preheat your oven to 400°F (200°C), ensuring it’s fully heated by the time your batter is ready.

This helps the muffins rise nicely in the oven.

Step 2: Mix the Dry Ingredients

• 1 1/2 cups whole wheat flour
• 1/2 cup plain flour
• 3/4 cup packed light brown sugar
• 1 tbsp baking powder
• 2 tsp baking soda
• 2 tsp pumpkin pie spice
• 1/2 tsp ground cinnamon
• 1/2 tsp salt

In a medium bowl, combine the whole wheat flour, plain flour, packed light brown sugar, baking powder, baking soda, pumpkin pie spice, ground cinnamon, and salt.

Whisk these together until everything is evenly distributed and makes a uniform mixture.

This will ensure your muffins have a consistent texture and flavor.

Step 3: Mix the Wet Ingredients

• 3/4 cup pure pumpkin (not pie filling)
• 1/4 cup unsweetened applesauce
• 1/2 cup melted coconut oil
• 1 large apple, coarsely grated
• 1 tbsp vanilla extract
• 2 cups grated carrots (from about 3 medium carrots)

In a large bowl, add the pure pumpkin, unsweetened applesauce, melted coconut oil, coarsely grated apple, vanilla extract, and grated carrots.

Whisk everything together until well combined.

This mixture should look glossy and evenly mixed.

I like to use freshly grated apple and carrots for extra moisture and flavor.

Step 4: Combine Wet and Dry Mixtures

• dry ingredients (from Step 2)
• wet ingredients (from Step 3)

Gently fold the dry ingredients (from Step 2) into the wet mixture (from Step 3) using a spatula or large spoon.

Mix until just combined, being careful not to overmix as this can make the muffins tough.

Step 5: Fold in the Add-Ins

• 1/2 cup dried cranberries
• 1/2 cup shredded coconut
• 1/2 cup chopped pecans

Add the dried cranberries, shredded coconut, and chopped pecans to the batter.

Gently fold these add-ins through the mixture, distributing them evenly.

Try not to stir too much to keep the muffins light and fluffy.

I love the texture and flavor these add-ins give—don’t skip them!

Step 6: Portion and Bake the Muffins

• batter with add-ins (from Step 5)

Scoop the batter evenly into the prepared muffin tin, filling each cup about three-quarters full.

Bake in the preheated oven for 24 to 28 minutes, or until a toothpick inserted in the center of a muffin comes out clean or with just a few crumbs.

The tops should turn lightly golden.

For perfectly moist muffins, I like to check at the minimum bake time and adjust as needed.

Step 7: Cool and Serve

Let the muffins cool in the tin for 10 minutes.

Then, remove them and transfer to a wire rack to cool completely.

Serve the muffins warm, at room temperature, or chilled according to your preference.

These are delicious any way you serve them, and they store well for a couple of days.

Irresistible Apple Pumpkin Breakfast Muffins

Delicious Irresistible Apple Pumpkin Breakfast Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 14 minutes mins

Cook Time 29 minutes mins

Total Time 43 minutes mins

Servings 4

Calories 2600 kcal

Ingredients

  

• 1 1/2 cups whole wheat flour
• 1/2 cup plain flour
• 3/4 cup packed light brown sugar
• 1 tbsp baking powder
• 2 tsp baking soda
• 2 tsp pumpkin pie spice
• 1/2 tsp ground cinnamon
• 1/2 tsp salt
• 3/4 cup pure pumpkin (not pie filling)
• 1/4 cup unsweetened applesauce
• 1/2 cup melted coconut oil
• 1 large apple, coarsely grated
• 1 tbsp vanilla extract
• 2 cups grated carrots (from about 3 medium carrots)
• 1/2 cup dried cranberries
• 1/2 cup shredded coconut
• 1/2 cup chopped pecans

Instructions

 

• Line a 12-mold muffin tin with paper liners and set aside. Preheat your oven to 400°F (200°C), ensuring it's fully heated by the time your batter is ready. This helps the muffins rise nicely in the oven.
• In a medium bowl, combine the whole wheat flour, plain flour, packed light brown sugar, baking powder, baking soda, pumpkin pie spice, ground cinnamon, and salt. Whisk these together until everything is evenly distributed and makes a uniform mixture. This will ensure your muffins have a consistent texture and flavor.
• In a large bowl, add the pure pumpkin, unsweetened applesauce, melted coconut oil, coarsely grated apple, vanilla extract, and grated carrots. Whisk everything together until well combined. This mixture should look glossy and evenly mixed. I like to use freshly grated apple and carrots for extra moisture and flavor.
• Gently fold the dry ingredients (from Step 2) into the wet mixture (from Step 3) using a spatula or large spoon. Mix until just combined, being careful not to overmix as this can make the muffins tough.
• Add the dried cranberries, shredded coconut, and chopped pecans to the batter. Gently fold these add-ins through the mixture, distributing them evenly. Try not to stir too much to keep the muffins light and fluffy. I love the texture and flavor these add-ins give—don't skip them!
• Scoop the batter evenly into the prepared muffin tin, filling each cup about three-quarters full. Bake in the preheated oven for 24 to 28 minutes, or until a toothpick inserted in the center of a muffin comes out clean or with just a few crumbs. The tops should turn lightly golden. For perfectly moist muffins, I like to check at the minimum bake time and adjust as needed.
• Let the muffins cool in the tin for 10 minutes. Then, remove them and transfer to a wire rack to cool completely. Serve the muffins warm, at room temperature, or chilled according to your preference. These are delicious any way you serve them, and they store well for a couple of days.