Best Breakfast Apple Muffins

Let’s face it – finding time to make a proper breakfast on busy mornings can feel nearly impossible. Between packing lunches, getting everyone dressed, and trying to get out the door on time, the last thing anyone wants to do is spend precious minutes in the kitchen whipping up something from scratch.

That’s where these breakfast apple muffins come to the rescue. They’re quick to prep ahead on weekends, perfectly portable for eating on-the-go, and just sweet enough to make mornings feel a bit more special. Plus, they’re a great way to use up those extra apples sitting in your fruit bowl.

What Kind of Apples Should I Use?

For muffins, you’ll want to pick apples that hold their shape when baked and offer a good balance of sweet and tart flavors. Honeycrisp, Granny Smith, Pink Lady, or Braeburn apples are all excellent choices for baking – they won’t turn mushy and will maintain their flavor. When you’re grating the apples, don’t worry if they start to brown a little bit since they’ll be mixed into the batter right away. Just make sure to peel them first, as the skin can create an unpleasant texture in your finished muffins. If you’re looking to save time, you can use the large holes of a box grater or even the grating attachment on your food processor to prep the apples quickly.

Options for Substitutions

These muffins are pretty forgiving when it comes to swaps! Here are some helpful substitutions you can try:

• Whole wheat flour: You can use all-purpose flour instead of whole wheat flour in equal amounts. For a gluten-free version, try a 1:1 gluten-free flour blend that contains xanthan gum.
• Applesauce: If you’re out of applesauce, try mashed banana or pumpkin puree in the same amount. This might slightly change the flavor, but will keep the muffins moist.
• Maple syrup: Honey works great as a replacement for maple syrup in equal amounts. You could also use brown sugar, but you’ll need to add an extra 3 tablespoons of liquid (milk or water).
• Coconut oil: As mentioned in the recipe, you can swap this with vegetable oil or melted butter in the same amount. Melted ghee works too!
• Allspice: No allspice? Use an equal amount of nutmeg, or try a mix of nutmeg and cloves (¼ teaspoon each).
• Nuts: The nuts are optional, but you can also try sunflower seeds or pumpkin seeds if you want a nut-free option. Or toss in some raisins or dried cranberries instead!

Watch Out for These Mistakes While Baking

The biggest challenge when making apple muffins is dealing with excess moisture – be sure to squeeze out the extra liquid from your shredded apples using a clean kitchen towel or cheesecloth, otherwise your muffins might turn out dense and gummy. A common mistake is overmixing the batter; once you combine the wet and dry ingredients, stir just until no flour pockets remain, as overmixing will lead to tough, rubbery muffins. Temperature matters more than you might think – using cold ingredients straight from the fridge can cause your coconut oil to solidify into lumps, so make sure your eggs, applesauce, and maple syrup are at room temperature before starting. For the perfect dome-shaped tops, fill your muffin cups almost to the brim and start baking at 425°F for 5 minutes, then reduce to 350°F for the remaining time – this initial blast of heat helps create that coveted muffin top.

What to Serve With Apple Muffins?

These cozy apple muffins make a perfect breakfast or brunch treat, and they pair wonderfully with a hot cup of coffee or tea. For a more filling breakfast, serve them alongside some Greek yogurt topped with honey and granola, or pair them with scrambled eggs and crispy bacon for a complete morning meal. If you’re hosting brunch, these muffins work great on a spread with fresh fruit salad and a pitcher of warm spiced apple cider or cold apple juice to play up those apple flavors.

Storage Instructions

Counter Storage: These apple muffins stay fresh at room temperature for 2 days when kept in an airtight container. I like to line the container with a paper towel to absorb any extra moisture – this helps keep the muffins from getting too soft.

Refrigerate: Want them to last longer? Pop your muffins in the fridge in a sealed container, and they’ll stay good for up to 1 week. The paper towel trick works great here too!

Freeze: These muffins are perfect for freezing! Let them cool completely, then place them in a freezer bag or container. They’ll keep for up to 3 months. When you’re ready to eat one, just let it thaw overnight in the fridge or pop it in the microwave for about 30 seconds.

Warm Up: While these muffins taste great at room temperature, you can give them a quick 10-second warm-up in the microwave if you want that fresh-from-the-oven feeling. They’re especially nice warmed up with a pat of butter!

Preparation Time	15-20 minutes
Cooking Time	21-23 minutes
Total Time	36-43 minutes
Level of Difficulty	Easy

Estimated Nutrition

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

• Calories: 1400-1600
• Protein: 20-25 g
• Fat: 60-70 g
• Carbohydrates: 200-220 g

Ingredients

• 2 cups whole wheat flour
• 1 tsp baking powder
• 1 tsp baking soda
• 2 tsp ground cinnamon
• 1/2 tsp allspice
• 1/2 tsp salt
• 2 large eggs, room temperature
• 3/4 cup unsweetened smooth applesauce, room temperature
• 2/3 cup pure maple syrup, room temperature
• 1/3 cup melted coconut oil (or vegetable oil or melted butter)
• 1 1/2 tsp pure vanilla extract
• 2 cups grated or shredded apple (about 2 peeled apples)
• Optional: 3/4 cup chopped walnuts or pecans
• Optional: 1 tbsp coarse sugar for topping

Step 1: Prep the Oven and Muffin Pan

Preheat your oven to 425°F (218°C).

Prepare a 12-count muffin pan by spraying it with nonstick spray or lining it with cupcake liners.

Set the pan aside until you’re ready to fill it.

I always make sure the oven is completely preheated before mixing the batter to ensure the muffins rise properly.

Step 2: Mix Dry Ingredients

• 2 cups whole wheat flour
• 1 tsp baking powder
• 1 tsp baking soda
• 2 tsp ground cinnamon
• 1/2 tsp allspice
• 1/2 tsp salt

In a large bowl, combine the whole wheat flour, baking powder, baking soda, ground cinnamon, allspice, and salt.

Whisk these dry ingredients together thoroughly so all the leavening agents and spices are evenly distributed.

Set this bowl aside for later.

Step 3: Mix Wet Ingredients

• 2 large eggs, room temperature
• 3/4 cup unsweetened smooth applesauce, room temperature
• 2/3 cup pure maple syrup, room temperature
• 1/3 cup melted coconut oil (or vegetable oil or melted butter)
• 1 1/2 tsp pure vanilla extract

In a separate medium bowl, whisk together the eggs, applesauce, pure maple syrup, melted coconut oil (or your chosen substitute), and vanilla extract.

Make sure all the wet ingredients are at room temperature and well combined for an even batter.

Step 4: Combine Wet and Dry Ingredients, Add Apples and Nuts

• wet ingredients (from Step 3)
• dry ingredients (from Step 2)
• 2 cups grated or shredded apple (about 2 peeled apples)
• optional: 3/4 cup chopped walnuts or pecans

Pour the wet ingredients from Step 3 into the bowl of dry ingredients from Step 2.

Stir the mixture a few times (do not overmix), then add the grated or shredded apples and, if desired, the chopped walnuts or pecans.

Use a silicone spatula to gently fold everything together just until no streaks of flour remain.

The batter should be very thick.

I like to be gentle at this step to keep the muffins tender and fluffy.

Step 5: Fill Muffin Pan and Bake

• batter (from Step 4)
• optional: 1 tbsp coarse sugar for topping

Spoon the thick muffin batter into the prepared liners, filling them all the way to the top.

If using, sprinkle tops evenly with coarse sugar for a nice crunch.

Bake at 425°F for 5 minutes, then without opening the oven, reduce the temperature to 350°F (177°C) and continue baking for another 16–18 minutes, or until a toothpick inserted in the center comes out clean.

The total baking time is about 21–23 minutes.

(For mini muffins, bake at 350°F for 11–14 minutes instead.)

Step 6: Cool and Serve

Allow the muffins to cool in the muffin pan for 5 minutes before transferring them to a wire rack to cool completely, or enjoy them warm if you prefer.

I find muffins taste best slightly warm, and a little extra maple syrup drizzled on top makes for a wonderful treat.

Store leftovers covered at room temperature for a few days or in the refrigerator for up to 1 week!