Healthy Apple Muffins
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Healthy Apple Muffins that are easy to make and low calorie. Made with cinnamon, greek yogurt & whole wheat flour – they’re so yummy! This post is sponsored by my friends at Bob’s Red Mill.
This post was originally shared in August of 2018 but has been updated.
Apple season = the best season in my opinion. There are few things I love more than baking with apples, whether it’s these muffins, Healthy Baked Apples or Apple Oatmeal!
I’m the type of person that eats apple cinnamon and pumpkin flavored things all year round because I love them so much, but there’s something about enjoying fall flavored baked goods on a cool autumn day that makes them taste even better!
I have so many fond memories of going apple picking every fall with my mom and brother. Usually, we’d go with cousins or friends, and we would come back with WAY more apples than we could ever eat.
Lots of muffin recipes are loaded with sugar and sweeteners; these are sweetened with just apples and a bit of brown sugar, with some flavorful spices. You probably have everything you need on hand to make these healthy muffins!
Enjoy these for breakfast or as a snack. You totally could even warm one up, serve it with ice cream and call it dessert!
liz’s top tips for healthy apple muffins
- Don’t overmix your batter for light and fluffy muffins.
- You can double the batch and freeze half of them for the school year for an easy after-school snack kids will love. You can do the same with our pumpkin spice muffins.
- They’re also perfect for defrosting in the microwave, slathering with peanut butter, and heading out the door with (or enjoying in the afternoon with a cup of coffee… or pumpkin spice latte!)
Ingredients
You’ll also want to have a muffin tin, silicone muffin liners, and a blender.
All of the ingredients for this recipe are easily found on Thrive Market! Click here to get 30% off your first order and a free gift.
Substitutions
You can easily substitute many ingredients in this recipe. Here are some suggestions for you.
Apples: We haven’t tried this recipe with other fruit but I think pears would work interchangeably here. You can check out our Healthy Blueberry Muffin Recipe or Healthy Zucchini Bread Muffins if you’re looking for other healthy muffin recipes.
Applesauce: We don’t recommend substituting the applesauce. Banana or pumpkin might work, but we can’t recommend it.
Oil: You can use extra virgin olive oil, vegetable oil, avocado oil, or melted butter.
Maple Syrup: You can substitute maple syrup for honey.
Brown Sugar: You can substitute coconut sugar but it is not as good! Brown sugar and coconut sugar have the exact same amount of calories.
Nonfat Greek Yogurt: We do not recommend substituting Greek yogurt in this recipe. It tenderizes the whole wheat flour and works as buttermilk would.
Egg free: I have not tried making these muffins egg free. I think subbing flax eggs would work, but I’m not sure.
Milk: You can use any regular dairy milk or oat milk in place of the almond milk.
Whole Wheat Flour: We don’t recommend using other flours in this recipe. Bob’s Red Mill Gluten Free 1:1 may work but we haven’t tried it so can’t be sure, it may affect the texture.
Protein: If you are looking to up your protein intake, try our Apple Protein Muffins.
How to make healthy Apple Muffins
- In a bowl whisk together applesauce, oil, maple syrup, eggs, brown sugar, vanilla, Greek yogurt, and milk. Stir in your dry ingredients.
- Gently fold in the diced apple chunks with a spatula.
- Add muffin liners to a muffin pan. Scoop the muffin batter mixture into 12 muffin cups.
- Bake at 425° for 5 minutes then turn down to 350° for 14 minutes or until a toothpick inserted in the center comes out clean.
I love baking with Bob’s Red Mill products because it’s a brand I trust with high quality ingredients.
By now I’m sure you’ve seen me use their flour in these Healthy Banana Muffins or Healthy Pumpkin Bread or their regular flour in the Italian Cream Pie!
What kind of apples are best for baking?
Any apple will work for baking, but different apples have different tastes.
If you prefer sweeter apples, Cortland, honeycrisp, or Fuji are a good choice. For a more tart apple muffin, granny smith apples, Braeburn, McIntosh are a better choice.
This post lists all of the different apples and flavors they bring to a dish.
There’s really no ‘wrong’ apple to use – when you bake apples they become softer, sweeter + sooo delicious!
Storage options
Storing: I store these healthy apple cinnamon muffins in an airtight container in the fridge for up to a week to maintain freshness. You can leave them out of the fridge on the counter, but they will only last about 3-4 days.
Freezing: You can freeze these muffins and they will last for about 3 months in the freezer. Put the muffins in an airtight container or ziploc bag. To defrost, leave out the night before in the fridge and they will thaw out. Or – just pop it in the microwave for 1-2 minutes!
Other healthy muffin recipes:
Healthy muffins are the best! Check out these Healthy Muffins, or these:
Healthy Apple Muffins
Ingredients
- ⅓ cup applesauce
- ⅓ cup melted coconut oil
- ⅓ cup maple syrup
- ¼ cup brown sugar
- 2 teaspoons vanilla extract
- ⅓ cup nonfat Greek yogurt
- 2 eggs
- ¼ cup unsweetened vanilla almond milk
- 2 cups Bob's Red Mill Whole Wheat Flour
- 1 teaspoon ground cinnamon
- 1.5 teaspoons baking powder
- ½ teaspoon baking soda
- ⅛ teaspoon salt
- 2 cups apples thinly sliced then chopped into small pieces about 2 apples -you don’t want chunks
Streusel Topping (Optional)
- 1 tablespoon melted butter
- 1 teaspoon ground cinnamon
- 1/4 cup sugar
Instructions
- Preheat oven to 425.
- In a bowl mix together applesauce, oil, maple syrup, eggs, brown sugar, vanilla, Greek yogurt and milk.
- Once it’s combined add in the 2 cups of whole wheat flour (add half cup at a time until just mixed), cinnamon, baking powder, baking soda, and salt.
- Gently fold in the apple chunks with a spatula.
- Optional: Mix together topping ingredients.
- Add muffin liners to a muffin tin. Spray with cooking spray for good measure . These muffins rise high and the edges can stick if you don’t spray the whole tin.
- Scoop the muffin batter into 12 muffin cups.
- Add the streusel topping just evenly distributing it onto each muffin.
- Bake at 425 degrees for 5 minutes then turn the oven down to 350 for 14 minutes or until a toothpick inserted in the center comes out clean. Important: the different temperatures allow this muffin to rise high!
- Allow to cool for 15 minutes on a wire rack. Enjoy.
These are so delicious! I baked them several minutes less than recommended because I like them more moist. 1/2 I put the topping on and other 1/2 I left it off for a less sweet version.
I doubled the recipe and froze 1/2 and that works very well!
These look delicious and I think our kids will love them! Question on the flour – your note in the ingredient list says not to use the stone ground version, but that is all I can find when I search Bob’s Red Mill Whole Wheat flour, and your link above takes me to an Amazon listing that shows Bob’s Red Mill 100% stone ground Whole Wheat Flour. Is that what we should use? So excited for fall and apples in season, keep the apple recipes coming!
Sorry about that – I just updated the blog post, that was a typo! Hope you enjoy these muffins 🙂 Our Healthy Apple Crisp recipe is delicious too!
I was looking for a healthy recipe to bake with my 2 and 4 yrs old grandsons. This sounds like it will be perfect!! The ingredients for the streusel topping- are there only 3 ingredients: butter, cinnamon and sugar? If so, could I safely add a 1/4 cup of oatmeal to the mixture?
I’m sorry but I haven’t tried adding oatmeal to it, but I think it would work!
So easy to make! Delicious! Moist and huge muffins! My teenager refused cereal, so I am baking something for him every weekend! These will be on repeat! Curious how macros would change and if they would be as soft and moist if protein powder was added. Liz & Tyler – Great work here! These will be on repeat in my house and would be great gifts for someone under the weather or recuperating as we see the New England weather turn and apple picking at his height!
I’m so glad you liked them, Christine! I honestly don’t know how protein powder would work in these muffins. I want to make a protein apple muffin but haven’t got around to testing it. Check out our pumpkin protein muffins – those are so yummy nad have 9g of protein per serving! I think if you subbed pumpkin with apple sauce it might work, but I can’t be sure without trying.
So good! I couldn’t stop eating them!
Absolutely loved these! Even used the fresh made applesauce recipe in them! I used gala and autumn crisp apples. Problem is I had no will power to control how many I ate so lol
Made this GF,DF it was moist and yummy
I see some comments about rolled oats, but I don’t see oats listed in the recipe. Are they using rolled oats instead of the wheat flour?
I’m not sure! We don’t recommend using other flours in this recipe. Bob’s Red Mill Gluten Free 1:1 may work but we haven’t tried it so can’t be sure.
Can I use regular yougurt instead I live in canada and greek yougurt is too expensive.
I think that would work! I haven’t tried it so I’m not sure!
Very good. Easy to put together. They were soft and sweet. I followed the recipe exactly. I might cut back on the sugar or syrup next time. I like muffins that are barely sweet, but that is just a personal preference. My husband and two toddlers loved them. I will make them again.
LOVED these. I added some chopped walnuts to the mix b/c I love nuts in my muffins. I also added some rolled oats to the streusel topping and it was crunchy and so good!!!!
So happy you liked them!