Whole wheat apple muffins are hearty and fluffy with hints of sweet baked apples. This is a simple muffin made from whole wheat flour, honey, cinnamon, eggs, milk, and oil. Everything is mixed together to form a batter, then baked in muffin cups until golden brown.

Serve as a quick and healthy breakfast, or as healthy snacks with tea, coffee or a smoothie. If you love muffins like we do, then you might also want to try our popular Baked oatmeal breakfast cups with six delicious flavors or our rhubarb whole wheat muffins which have a sweet and tart taste.

Whole wheat apple muffins piled into a bowl lined with a linen kitchen towel.

Healthy Apple Muffins

These muffins can be put together fast using wholesome ingredients you probably already have in your kitchen.
Whole wheat flour gives these muffins a heartier texture, but can easily be swapped with all-purpose flour if desired.
This is the perfect recipe to make with in-season ripe crisp apples. Feel free to use your favorite apple variety.
These can be baked in 20 minutes. Just dump ingredients into a bowl with chopped apples (or grated apple), add batter to a muffin pan and bake.
Make a double batch and store extra in the freezer!
We love muffins and have many muffin recipes including our easy oatmeal muffins with six flavors and delicious blueberry yogurt oat muffins.

Recipe Ingredients

APPLES: Many people enjoy granny smith apples with baking muffins because of their tart flavor (they taste delicious combined with the sweetness from the muffin). I used pink lady apples which are crisp and tangy sweet. Other fresh apples that can also be used including fuji, gala and honey gold. There’s no need to peel the apples before adding them to the recipe. The skin can be left on.

Want more apple recipes? Try our easy and delicious apple crisp or our easy applesauce cookies.

DRY INGREDIENTS: Whole wheat pastry flour (or regular whole wheat flour) is mixed with cinnamon, baking powder, baking soda, and salt. If preferred, divide the flour using 1 cup whole wheat flour and ¾ cups white all-purpose flour.

WET INGREDIENTS: Milk, vegetable oil, and one egg are mixed in with the dry ingredients. This recipe can be made with dairy-free milk such as almond milk, oat milk, soy milk etc. You can also substitute the oil for olive oil, coconut oil, avocado oil or melted butter.

VARIATIONS: Substitute half of the apples with a different apple style for variation. Or use 1 cup apples and 1 cup fruit or dried fruit (raisins, chopped apricots etc.) Try adding chopped nuts or seeds for a heartier texture. Or try 1 cup whole wheat flour and ¾ cup all-purpose flour for a fluffier consistency.

Four images showing steps to make recipe including chopped apples with a knife. A bowl of chopped apples mixed in honey with a spatula. Muffin batter with chopped apples in a bowl with a wood spoon. A muffin pan with paper liners and batter in each cup.

How To Make Whole Wheat Apple Muffins

A quick overview of how to make these delicious apple muffins with full instructions in the recipe card below.

Stir chopped apples with honey in a small bowl. Set this aside.
Add whole wheat flour, cinnamon, baking powder, baking soda and salt together in a large mixing bowl.
Add milk, egg and oil together in a separate bowl. Make a well in the center of dry ingredients and add the wet ingredients. Mix everything together. Fold the apple chunks into the batter.
Add paper liners to the muffin tin and fill with ¾ of batter. Bake muffins until tops are golden and a toothpick comes out clean.

Leftover muffins can be stored in an airtight container at room temperature or chilled in the fridge up to 3-4 days. These muffins also freeze well. Add them to a freezer bag and store up to 3 months for maximum freshness. Frozen muffin can be thawed in the microwave for 30 seconds to warm and served with a little butter.

A dozen baked whole wheat apple muffins in a muffin pan.

Recipe Tips

Don’t forget to measure 2 cups of chopped apple into the batter. Do not add two full apples to the batter unless that measures 2 cups. Otherwise, there will be too many apples.
Chop the apples into small bite-size pieces. If they’re too big, the muffins won’t cook correctly.
Check the muffins for around 19 or 20 minutes to see if the tops are starting to turn golden brown.
If muffins are sticking to the paper cupcake liners, lightly spray the insides with nonstick cooking spray before adding the muffin batter.
Don’t overfill the muffin cups. Fill them ¾ full so there is room for them to rise.

Close up of six apple muffins lined side-by-side.

More Muffin Recipes

Lemon Blueberry Muffins are sweet and zesty using fresh blueberries and lemon rind.
Applesauce Oatmeal Muffins have a hint of warming Fall spices. These healthy muffins are moist and fluffy.
Whole Wheat Buttermilk Muffins are a high fiber breakfast idea.
Cottage Cheese Muffins have a fluffy texture – you can’t taste the cottage cheese at all. One of my favorites.
Flaxseed Muffins are high in fiber with healthy ingredients. These use ground flaxseed instead of flour.