Healthy Cinnamon Apple Muffins

Created On: June 18, 2020 | Updated: September 8, 2026 | 33 Comments

These healthy cinnamon apple muffins have been a reader favorite for years. They’re soft, fluffy, perfectly spiced, and packed with apple flavor, but they’re made with whole wheat flour, olive oil, and honey instead of loads of butter and sugar.

They don’t taste “healthy” at all. The texture is incredibly moist and tender, and there are tested gluten-free and dairy-free options, too.

I’ve been making the whole wheat version for over 15 years now, and they’re still one of my favorite muffins to bake during apple season.

What’s To Love

Made with wholesome ingredients
Super moist and fluffy
Whole wheat and gluten-free options
Easy dairy-free option
Perfectly spiced
Great for breakfast or snacks

Ingredient Notes

Please scroll down for the full recipe. These are just notes on select ingredients.

Flour – I’ve successfully made these with whole wheat flour, white whole wheat flour, whole spelt flour and all-purpose flour, and all four versions taste the same. For the gluten-free version, use 1 cup (138 grams) Bob’s Red Mill Gluten-Free 1-to-1 Baking Flour. That’s the gluten-free flour I tested here, and it gives the muffins a great texture without being gummy or gritty.
Oil – I’ve successfully used extra-virgin olive oil, canola oil and refined coconut oil. You may notice the extra-virgin olive oil flavor in the batter. With the gluten-free and all-purpose versions, you may also notice it while the baked muffins are still warm, but it disappears once they cool completely. If you’re sensitive to olive oil flavor, use a lighter olive oil or another neutral-tasting oil. Use refined coconut oil if you don’t want coconut flavor.
Honey – the muffin base uses 1/3 cup (106 grams) honey. Maple syrup would very likely work, although I haven’t tested it. One reader reduced the honey to 1/4 cup and reported that the muffins were still nice and moist, although they’ll be less sweet.
Yogurt or buttermilk – either works well, but you do need an acidic ingredient for the baking soda to work properly. Vanilla yogurt should also work, although it will make the muffins a little sweeter. For a dairy-free version, use dairy-free yogurt or homemade dairy-free buttermilk.
Apples – use 1 cup (120 grams) of apple cut into roughly 1/4-inch pieces. A firm baking apple such as Granny Smith works well. Blueberries or raspberries would probably work instead, although I haven’t tested them. I don’t recommend replacing the diced apple with applesauce without reworking the recipe, and I haven’t tested grated apple.
Spices – cinnamon, nutmeg and allspice help balance the whole wheat and olive oil flavors. I really recommend keeping the cinnamon and nutmeg, but the allspice is optional. If you omit the nutmeg, increase the cinnamon to 2 teaspoons.
Egg – I haven’t personally tested a flax or chia egg and have had problems with egg replacements in other muffin and cake recipes, so I can’t guarantee them here. One reader successfully used 3 tablespoons of Just Egg.

If you use extra-virgin olive oil, don’t worry if you notice the flavor in the batter. The same thing happens with my Healthy Chocolate Cake and Healthy Applesauce Muffins. The flavor mellows as the muffins bake and cool.

You can leave these muffins plain, sprinkle them with cinnamon sugar, or add streusel. Without a topping, the muffin base is sweetened only with honey. The streusel is generous, and brown sugar or coconut sugar both work. The wheat and gluten-free versions use different streusel recipes, so follow the appropriate version in the recipe card.

How to Make Healthy Cinnamon Apple Muffins

Prepare the streusel, if you’re using it.
Whisk together the dry ingredients. In another bowl, stir together the wet ingredients. Add the dry ingredients to the wet ingredients and mix just until combined. Gently fold in the diced apples.
Divide the batter among 9 muffin cups.
Add the streusel or cinnamon sugar if using, and bake until a toothpick inserted into the center comes out clean.

Tips for Success

Don’t overmix the batter or the muffins can turn out dense.
If using extra-virgin olive oil, let the muffins cool completely before judging the flavor.
Cut the apples into pieces about 1/4 inch in size so they cook evenly throughout the muffins.
Use a firm baking apple such as Granny Smith.
Measure the flour carefully and avoid packing it into the measuring cup.
You can make these plain, with cinnamon sugar, or with streusel topping.

Gluten-Free and Dairy-Free Options

For the gluten-free version, use Bob’s Red Mill Gluten-Free 1-to-1 Baking Flour. The muffins turn out soft and moist without being gummy or gritty.

To make the muffin base dairy-free, use dairy-free yogurt or homemade dairy-free buttermilk. I’ve used coconut milk yogurt with great results, and the muffins didn’t taste coconutty at all.

For homemade dairy-free buttermilk, add 3/4 teaspoon lemon juice, white vinegar or apple cider vinegar to a 1/4-cup measuring cup. Fill the rest of the measuring cup with dairy-free milk and let it sit for 5 minutes.

If you’re adding a topping, keep in mind that the wheat streusel contains butter. The gluten-free streusel uses coconut oil. For a dairy-free wheat version, leave the muffins plain or use the cinnamon-sugar topping.

The muffins pictured above are the gluten-free version. The whole wheat version is darker in color, like the older photo below. This recipe originally appeared on my other site, Texanerin Baking, which is why that photo is watermarked texanerin.com.

The streusel also looks different because the gluten-free version uses a different streusel recipe. I find streusel difficult to convert to gluten-free, so I used a recipe that I already knew worked well.

If you love apples and cinnamon as much as I do, this Apple Cinnamon Oatmeal is another great breakfast option.

Make Ahead and Storage

Once completely cooled, store the muffins in an airtight container at room temperature for up to 4 days. After that, store them in the refrigerator.

The whole wheat version actually gets even softer and moister on the second day, which makes these a great option when you want to bake breakfast ahead of time.

More Muffin Recipes

These Apple Cranberry Bran Muffins are another wholesome apple breakfast.
These Spelt and Oat Pear Muffins are another whole-grain fruit muffin.
Try these Sourdough Cinnamon Muffins for another warmly spiced muffin.

❤️ Have you tried these healthy cinnamon apple muffins? ❤️

Please leave a ✍️ review and ⭐ rating to let me know how they turned out. I appreciate it so much! 💛

5 from 45 votes (43 ratings without comment)