These healthy apple oatmeal muffins are the perfect fall breakfast recipe or after-school snack. Grab your kiddos, and whip up a batch in the kitchen today (really, a double-batch because they freeze beautifully)!Some people might call our current month September, but I call it…APPLE SEASON! The weather around here has been cooling off, and I’ve been waking up to crisp mornings that have very much put me in the mood for baking. At the top of my “to bake” recipe list were today’s delicious apple oatmeal muffins.
I love a good muffin. There’s just something wonderful about biting into a warm, hearty muffin on a cold day. In my mind, the best way to cope with cold weather is to warm up from the inside out.Muffin recipes are not something new around here. My kids love these blueberry muffins and these banana chocolate-chip muffins. But with fall coming, I’ve been dying for a good apple muffin recipe–something we can keep on hand for after-school snacks or quick breakfasts.
This recipe is both super easy and full of healthy, hearty ingredients. It uses all whole grains, has only 1/4 cup coconut oil, and is sweetened with just a bit of maple syrup. But, don’t let the healthy ingredients trick you into thinking that these are going to be dry, tasteless muffins. Despite the fact that you can genuinely feel good about eating these, they are full of flavor and are super moist (sorry to those of you that hate that word, but it’s accurate).
The first time I made them for my kids to have as an after school snack, we all sat around like Bob Wiley saying, “Mmmm…MMMM…mmm…” (Please tell me you know that movie.) It was ridiculous…and really satisfying.
Before you get to baking your own batch, here are a few things to know…
What apples are best for muffins?
You can really use any variety, but obviously the taste of the apple will alter the taste of the muffins. Granny Smith will yield a more tart muffin, whereas Gala apples will be sweeter.
My favorite apple is the Honeycrisp variety (they have a great balance of sweet and tart that is perfect for baking), but be aware they tend to be a little more expensive.
What is the best way to store muffins?
If (and it’s a big IF) you don’t eat your entire batch of muffins within hours of them coming out of the oven, you need to think about how to store them. It makes me so sad when a delicious muffin gets stale or super soggy because it wasn’t stored properly. It’s such a waste of potential happiness (yep, I get dramatic about food).
After much trial and error, I’ve found that you can store muffins on the counter for up to two days if you put them in a zip top bag or an air-tight container. The KEY is to place a paper towel both under the muffins and over the tops of them to absorb moisture that evaporates from the muffin but gets trapped in the container. (Note: To limit condensation, make sure you let the muffins cool completely before placing them in a container for storage.)
If you want them to last more than a couple of days, freezing them is best. Read on for details…
Can I freeze apple oatmeal muffins?
Absolutely! In fact, when I make muffins I usually make them in batches of 24 so I can eat half of them fresh and freeze the other half to be used in the coming weeks. Here’s what you do:
- Let the muffins cool completely. If you don’t, condensation will collect as they cool and crystallize when it freezes (i.e. – your beautiful muffins will get horribly freezer-burned).
- Transfer muffins to an air-tight container (I use a gallon-sized ziploc freezer bag). Keep them in a single layer, or place wax paper/freezer paper between layers.
- Place them in the freezer and store for up to three months.
To thaw frozen muffins:
Option 1: Place them on the counter for a few hours (or overnight if you’re planning to use them for breakfast).
Option 2: Place a few muffins on a microwave safe plate and heat in 30 second intervals until the muffins are thawed and warm. (This is how I do it 90 percent of the time.)

Healthy Apple Oatmeal Muffins
These hearty and healthy apple oatmeal muffins are a perfect make-ahead breakfast or after-school snack.
Ingredients
- 1 cup wheat flour
- 1 cup quick oats
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon kosher salt
- 1 teaspoon cinnamon
- 2 cups apples, peeled and diced (*see note)
- ¼ cup melted coconut oil
- 2 large eggs
- ⅓ cup maple syrup (or honey)
- 1 teaspoon vanilla
- ½ cup applesauce
- ½ cup plain yogurt (I used Greek)
Instructions
- Preheat oven to 425°. Grease muffin tin or use paper liners.
- In a large bowl, mix together dry ingredients: flour, oats, baking powder, baking soda, salt, cinnamon. Add apples and toss to coat with the flour mixture.
- In a medium bowl, mix together wet ingredients: oil, eggs, syrup,vanilla, applesauce and yogurt. (If the coconut oil solidifies when it comes in contact with cold ingredients, you can warm the mixture in the microwave in 30 second increments until the oil melts again.)
- Pour wet ingredients into dry ingredients and mix gently until just combined (don’t overmix).
- Divide the batter between the 12 muffin cups--cups will be mostly full. If you want to be fancy, sprinkle a few oatmeal flakes on top for garnish (I like to use whole rolled oats for this).
- Put muffins in the oven and reduce oven temperature to 350°. Bake for 15-20 minutes, until the tops are golden and a toothpick inserted comes out clean.
- Let muffins cool on a wire rack, and enjoy!
- Store muffins in an airtight container at room temperature for a couple of days, or freeze them for up to 3 months.
Notes
You can use any kind of apple in these muffins. Granny Smith will yield a more tart muffin, whereas Gala apples will be sweeter. My favorite apple is the Honeycrisp variety (they have a great balance of sweet and tart that is perfect for baking), but they tend to be a little more expensive.
Also, if you loathe the tedious process of peeling, coring, and dicing apples...try this handy gadget. I'm not usually one for kitchen tools that only have one use, but this is one exception to the rule. Plus, my kids think it's super fun!
Source: Adapted from Cookie and Kate. Added oatmeal, and adjusted several other ingredient amounts.
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My muffins won’t cook in the middle. Cooked for 40 minutes and still not done. All the apples sunk to the bottom also. What did I do wrong? They smell delicious and the batter has a nice flavor. I was really looking forward to having them for my two year old granddaughter.
Jane, I’m so sorry these didn’t turn out for you! It sounds to me like your batter somehow ended up too wet. That would explain the sinking apples and the fact that they weren’t done all the way even after a longer cooking time. Double check that you didn’t add too much of one of the liquid ingredients (I’ve totally done that with recipes before…especially when I’m doubling them) or too little of a dry ingredient. Feel free to send me more info about your experience and I’ll be happy to try to troubleshoot with you!