Cozy fall muffins with a healthy twist! Naturally sweet and made with 100% whole grains, these tasty apple cinnamon oat muffins are an easy, high fiber snack the whole family will love. You’ll also love my gluten-free pumpkin bread, blender banana muffins, or protein pumpkin pancakes.

Charlotte’s 5-star review! ⭐️ “Love these muffins, just made my second batch.”
Why You’ll Love This Dietitian-Made Recipe
- Perfectly sweet and surprisingly moist. After gathering feedback from readers, I tweaked this recipe to be even more moist and satisfying, without sacrificing the health benefits.
- Nutritionally balanced. These apple cinnamon muffins are dietitian-designed to have more fiber, less sugar, and less saturated fat than other similar recipes. And they’re calorie-balanced — so you can feel good about enjoying these muffins yourself, and feeding them to your family.
- Incredibly easy. In just 30-minutes, you’ll have 12 delicious and crowd-pleasing muffins ready for the week. They’re quick, easy, and hard to mess up!
Dietitian spotlight 🔎 Wondering what makes these muffins healthy? They use whole wheat flour and rolled oats for the base for an extra fiber boost. And they’re also packed with wholesome ingredients like unsweetened apple sauce, Greek yogurt, and maple syrup for less fat and sugar than other options.
Key Ingredient Notes

- Maple syrup: Any liquid sweetener should work (honey is the best swap), but I prefer the flavor of maple syrup.
- Rolled oats: I like the texture of large flake rolled oats, but you can use quick oats in a pinch. I do not recommend swapping for instant oats or steel cut oats.
- Apples: I use honeycrisp, but braeburn, fuji, cortland, empire, golden delicious, and granny smith work too. Here’s more information to help you choose the right apples for baking.
Scroll down to the recipe card for the full ingredients list and detailed recipe.
Want more healthy snack recipes? Try my double-chocolate banana muffins, cookie dough protein balls, or chocolate baked oatmeal.
How to Make Apple Cinnamon Oat Muffins

Step 1: Whisk dry ingredients together.

Step 2: Whisk wet ingredients together in a separate bowl.

Step 3: Combine dry ingredients, wet ingredients, and apples and stir until just combined.

Step 4: Add to a lined muffin pan and bake!
Top Tips for Moist and Delicious Muffins
Whole wheat flour has a tendency to get tough and dry if not handled properly. Here’s what I learned after thoroughly testing this recipe for perfectly moist and light muffins:
- Don’t over-mix your batter. Over-working your batter will make your muffins tough and dry. Stir until just combined and stop there.
- Don’t bake for too long. Watch your muffins and remove them from the oven as soon as they’re ready. You’ll know they’re done when a toothpick inserted into the center comes out mostly clean with a few moist crumbs, and the tops look set. Remove them from the pan after 5-minutes of cooling, or they’ll continue cooking and dry out.
Common Questions
Let your muffins cool to room temperature before storing. Store in a sealed bag or airtight food container for up to three days on the counter. To keep them fresh longer, store in the freezer for up to three months and defrost on the counter overnight before eating.
You can, but I don’t recommend it. They get more dry and a bit tough in the fridge, so it’s best to freeze them or keep at room temperature. If you have to refrigerate them, gently microwave for 10-15 seconds before eating.

More Healthy Muffin Recipes
- Chocolate Banana Muffins
- Whole Wheat Blueberry Muffins
- Honey Bran Muffins
- Black Bean Brownie Bites
- High Protein Blueberry Muffins
Explore more healthy snacks and healthy muffins recipes!
If you made these healthy apple cinnamon oat muffins, leave a 5-star rating ⭐️ below. Don’t forget to follow me on Instagram!

Healthy Apple Cinnamon Oat Muffins
Equipment
- 12 Muffin liners (paper and silicone both work)
- 3-Tbsp cookie scoop (optional)
Ingredients
- 1 ½ cup whole wheat flour, spooned and levelled
- ¾ cup rolled oats
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1 tsp salt
- 2 tsp cinnamon
- 6 Tbsp unsalted butter, melted and cooled to room temperature
- ½ cup maple syrup
- ½ cup unsweetened apple sauce
- ½ cup plain Greek yogurt
- 2 tsp vanilla extract
- 2 large eggs
- 1 cup finely chopped apple, about one small apple with skin on
Instructions
- Position oven rack to the middle and pre-heat to 350 F. Line a 12-cup muffin pan with paper or silicone liners. Set aside.
- To a large bowl, add flour, oats, baking powder, baking soda, salt, and cinnamon. Whisk and set aside.
- To a separate large bowl, add melted butter, maple syrup, apple sauce, Greek yogurt, vanilla, and eggs. Whisk until smooth.
- Add dry ingredients and chopped apples to wet ingredients. With a large wooden spoon or spatula, mix until just combined. Be careful not to over-mix.
- Scoop batter into muffin liners, distributing evenly. I like to use a 3-Tbsp cookie scoop for this step to minimize mess.
- Transfer to the oven and bake for 18-22 minutes, or until tops are set and a toothpick placed in the center comes out mostly clean. Be careful not to over-bake these or they could dry out.
- Let muffins cool in the pan for 5-minutes before transferring to a wire rack. Cool to room temperature before eating.
Notes
- You can swap rolled oats for quick oats if needed.
- I use low-fat Greek yogurt, but whole milk works too.
- Honeycrisp apples are my favorite, but braeburn, fuji, cortland, empire, golden delicious, and granny smith will also work. Keep the skin on for extra fiber.
- To avoid dry and tough muffins, don’t over-mix your batter and be careful not to over-bake. Whole wheat flour is a little sensitive, so be gentle!
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.










Made these muffins tonight and they were delicious!. I did make some changes, instead of the 1/2 cup of unsweetened apple sauce, I bought a little jar (I believe 75g) of pure purรฉed apples. I used Granny Smith apples and removed the skin. I cooked at 175 C / 350 F for 17 minutes and 40 seconds – they were perfect.ย
Easy recipe to follow. I shredded my apples (and the juice from it) made my muffins super moist. It is a little dense, yet delicious. Going to make maple icing for a little sugar kick
These are really good. I made a few changes to make them healthier. I used applesauce instead of butter and honey in place of brown sugar. Applesauce qty is same but honey is 1/3 cup instead of 1/2. Turned out greatย
So glad you enjoyed, Leslie! And thanks for mentioning those swaps — always good to know what works!
Love these muffins, just made my second batch.
And definitely follow Mirandaโs recommendation to heat from frozen, on my last batch I noticed a difference between the ones I left in the fridge to eat vs the ones I heated up from frozen. I donโt know why but the latter is better!
Also, if these are coming out dry for you, itโs probably the whole wheat flour. ย When using whole wheat flour, let the batter rest for 20 to 30 mins after youโre done mixing everything. ย Then add a bit more milk to get the batter consistency you want and then fill the muffin tray. ย I added this step and they came out fluffy on my second batch.ย
I used coconut oil instead of butter and added walnuts. Delicious!
What a great swap! So glad you enjoyed. Thanks so much for your review!
I just made these muffins for the first time. My batter seemed dry and I was carefull not to over mix. So I added 2tsp of butter and almost 1/4cup of milk, the batter still seemed to have more moister but not real liquidity batter. I also, added 1/2tsp of nutmeg, ginger and 1/2 cup of chopped walnuts. Baked for 20 minutes and came out Good! I will make them again! Thanks
These were delicious after I added unsweetened applesauce. ๐
Thanks.
I will try this next, it look good