Want healthy meals your kids will love?

Healthy Apple Muffins


Made with whole wheat flour, coconut oil, applesauce and maple syrup these Healthy Apple Muffins will be your new favorite apple recipe.  

If you love fruit in your muffins, try our amazing Banana Muffins!

Are Muffins Healthy?

Muffins are an interesting food.  Sometimes grocery stores like to masquerade cake without frosting as a muffin.  So you think you’re getting something semi-healthy when really you’re just eating dessert.  Muffins are supposed to have a different texture than cake!  And these healthy apple muffins are made with no refined sugar, but with maple syrup instead.  A delicious muffin doesn’t need lots of sugar and fat.  This muffin really highlights the delicious taste of the apples instead of masking it with an overly sweet sugar flavor.   These apple muffins include fruit, but also nutrient dense ingredients like whole wheat flour, coconut oil, and walnuts.

Here are a few more tips for making a healthier muffin:

  1.  Use fruit to decrease some of the oil.  Applesauce is a great substitute for oil and adds a lot of moisture and flavor.
  2. Use whole wheat flour or half and half.  This adds fiber and lots of vitamins and minerals to your muffin.
  3. Add healthy add-ins to boost nutrition.  Chopped fruit, shredded veggies (like carrots or zucchini), nuts and dark chocolate chips all add great nutrition to your muffins.

What Apple variety is best for baking?

Does it matter what types of apple you use in baked goods?  Yes!  It affects the texture and how sweet your baked good is.  In a recipe like this, most of the sweetness will be based off your apple and so you will want to use a sweet apple.   I used Honeycrisp because I like the way they bake and they’re super sweet. Granny Smith is always a fine and safe option but they’re more on the tangy side, that’s why most people love to mix Granny Smith with sweeter apples in their pies.  There are plenty of great apple options, just find what your grocery store has available and these Healthy Apple Muffins will be a hit! You can also try our Healthier Caramel Apple Cake!

Here are a few more good apple varieties to use when baking:



Granny Smith



Golden Delicious



Nuts in Muffins

I used walnuts in this recipe because I love walnuts with all the warm fall flavors.  If you or your kids don’t love them like I do, then leave them out, it won’t affect the muffin recipe.  You can also swap the walnuts for a different type of nut.  I like to use nuts in muffins for the texture and the added protein.  It makes me feel fuller longer so I don’t end up snacking on whatever I can find 30 minutes later.   You can always chop up the nuts super fine if your kids aren’t wild about them.

What Can You Serve with Muffins for Breakfast?

You can serve these warm, cooled, with honey butter or jam.  We really like to serve our muffins with a side of eggs.  If you are in a hurry a boiled egg is a great choice.  But scrambled eggs pair well with these also.  If eggs aren’t appealing to your kids, then a smoothie with ingredients that includes protein is also a good choice.

How to Make the Best Apple Muffins

The difference between an amazing muffin and an ok muffin isn’t very many steps or time when you are making them.  If you follow some of these steps, your apple muffins will turn out amazing!

  1. Choose the right variety of apple
  2. If you want a full, rounded muffin then fill your muffin tin almost to the top.
  3. If you are going to fill your tins full, make sure you batter is pretty thick.  A thin batter will rise and run all over.
  4. Try to measure out the same amount of batter for each muffin so they will cook evenly.
  5. Don’t overmix your wet and dry ingredients!  If you overmix, then your muffin won’t be light and fluffy.

Can You Freeze Apple Muffins?

Muffins are one of our favorite foods to freeze.  It is so great to have a muffin on hand on a busy school morning with just 30 seconds of reheating.  These are tips we have found work really well to freeze and thaw muffins:

To Freeze:

  • Cool your muffins to room temperature.
  • Place muffins flat in your freezer for about an hour until they are mostly frozen before packing them in an airtight container.
  • Place your muffins in an airtight container like a ziploc bag or glass dish to keep air out.
  • Frozen muffins will stay good for up to 3 months.

To Thaw (a few different methods)

  1. Let your muffin thaw at room temperature.  Take about 30 minutes.
  2. Microwave for about 30 seconds.
  3. Wrap your muffin in foil and heat in the oven at 350°F for 10 minutes.

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4 from 226 votes

Healthy Apple Muffins

Made with whole wheat flour, coconut oil, applesauce and maple syrup these Healthy Apple Muffins will be your new favorite apple recipe.  
Prep Time10 minutes
Cook Time22 minutes
Total Time32 minutes
Course: Breakfast
Cuisine: American
Servings: 15 1 Muffin
Calories: 192kcal



  • Preheat oven to 425 degrees and line a muffin tin with cupcake liners or grease the wells.
  • In a bowl, combine flour, baking soda, baking powder, cinnamon and salt.
  • In a separate bowl, whisk together eggs, maple syrup, melted coconut oil, apple sauce and vanilla extract.
  • Pour the dry ingredients into the wet and slowly fold together.  Before it’s all combined, add grated apples and walnuts (or you can use pecans). Stir just until combined.
  • Fill muffin tins all the way to the top!  Bake at 425 degrees for 5 minutes and then decrease the temperature to 350 and bake for 12-18 minutes.  Bake until an inserted toothpick comes out clean.
  • Let cool and serve.


Calories: 192kcal | Carbohydrates: 26g | Protein: 4g | Fat: 9g | Saturated Fat: 5g | Cholesterol: 37mg | Sodium: 342mg | Fiber: 3g | Sugar: 12g
Keyword : Healthy Apple Muffins


Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

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Recipe Rating


I just made these with my son yesterday and they came out moist and delicious! Thank you for the recipe. I didn’t have coconut oil so I used melted butted instead without any issue.

Can I replace the whole weat flour for white flour? I know it won’t be as healthy but will they still have the right taste and texture?

My picky 10 year old eater has been loving these…I bumped up the cinnamon just a bit and went to one cup of maple syrup… more for my taste than his. Very moist. I want him to feel full in the morning at school, and this with a green juice on the side has been doing the trick.

Sadly, my 14 and 10 year old didn’t like them. They came out moist and fluffy but just not much flavor. Probably calls for more syrup and more salt. I also used Fuji apples, so that might have been part of the problem.

Thanks for sharing the idea 🙂

These sound great but my daughter is gluten free due to having Celiac disease. Do you think a gluten free flour would work in this recipe?

Thanks so much for the recipe – I can’t wait to try these. I’m just slightly confused by some of your amounts – I presume 5/2 teaspoon is 2.5 teaspoons, but what is 333/500 cup, and 3333/10000 cup and 333/1000 cup? (from a confused British person!)

Hi Lily, sorry about that! Yes, we’re having a technical issue with our recipe plugin today. We’re working on fixing it now. Thanks for your patience!

Hi Kelly, sorry for the confusion! We had some glitches to our recipes following a big update to our site last weekend. The amounts should look normal to you now. Thanks for your patience!

Hi there

I’m confused on the measuring of this (333/500 cup???) is it antypo or am I reading it wrong?

Hi Jenny, sorry for the confusion! We had some glitches to our recipes following a big update to our site last weekend. The amounts should look normal to you now. Thanks for your patience!

Crossing fingers they turn out great. I have them in the oven right now. I only used one apple and decided to finish off the rest with shredded carrot. Planning to send these in my kids lunches so wanted some added veg. Also threw in about 1/2C oats. I am hoping kids will love. You recipe looked fantastic and loved the maple syrup instead of all the sugars like in other recipes I was finding.

4 stars
Really liked this muffin. Need family to do a taste test too. Did you really mean “grated” apples or rather “shredded” apples? I started grating, but output looked just like raw applesauce, so I switched to shredding. This gave visible pieces of apples in muffins. I did not have coconut oil, so used vegetable – just fine. Left out nuts as not sure my 2 1/2 yr. old grand child could deal with those. I meant to add unsweetened shredded coconut in place of nuts, but totally forgot! Ended up with 13 muffins nice-sized muffins instead of 15.

Hi Maddy, that sounds good, and I’m glad you liked the muffins! Yes, I suppose “shredded” apples is right. (I’ve never considered the difference between grating and shredding!) Thanks for sharing.

I would like to use fewer EGGS in the recipe. Will the muffins turn out OK if I use ONLY 2 EGGS, and NOT 3 eggs?

Hi Sheila, you might get a slightly different texture but I think the muffins should still turn out with 2 eggs.

5 stars
Just made these, and WOW! They are fabulous! Muffins came out moist, and the texture was devine. A little crunch from the nuts and apple shreds. Perfect sweetness. Thank you for your diligence to create the perfect healthy apple muffin. We love them!

5 stars
Delicious! We ran out of maple syrup so substituted with honey and they turned out great. Kids have been eating them non-stop!

5 stars
I cut the recipe in half to make sure we liked them before committing. I wish I made the full batch! My 18m old is a picky one so we used just one tablespoon of cinnamon and apples we picked from the orchard. So happy to add to our healthy muffin recipe collection!

5 stars
These are delicious! I hadn’t found a whole wheat muffin recipe before this one that was so light. I like grating the apples because you can use the peelings. I’ll make this again!

3 stars
The prep time for this is way off unless I’m doing something totally wrong. Took me 30 minutes just to grate the apples!

Also followed the recipe to a T and they were a bit dry.

4 stars
Great muffins! We replaced the walnuts with flax seed meal since the kiddo’s school is nut free. The adults in the house will be adding these to our regular rotation of snacks to make. Thanks!

Tasted terrible. Can’t taste the appple , can’t taste the cinnamon, all I taste is salt. Moist cake full of 1 teaspoon of salt! Barely sweet at al, needs another half a cup of sugar if u have a sweet tooth

When grating the apples, mine were EXTREMELY juicy. I was worried it would make the muffins soupy so I strained them a bit. After baking I wondered if this was a mistake because they came out a bit dry. I thought the flavor was very yummy but too dry. Next time, should I leave all the juices from the apple?

5 stars
Absolutely love these muffins. They were super easy to make and they’re delicious. They’re also lovely and moist which I guess is due to the shredded apple. Will definitely make these again – I think they’ll become a staple actually.

5 stars
My favorite apple muffin recipe! I try a lot of different ones and keep coming back to this one. Love using maple syrup to sweeten and love that it uses applesauce to instill the apple flavor. My kids also love! I add some chia seeds and some cinnamon on top.

5 stars
I used one cup of ap flour and one cup of oat flour. I also substituted the maple syrup for honey. They were unbelievably delish!!

5 stars
Thank you for this recipe. I made them for my husband’s breakfasts at work. I used olive oil instead of coconut oil as my husband has heart disease. They came out wonderfully and we just love them!
Also, I used 1 cup of oats and 1 cup.of flour, along with maple syrup. Super duper muffins!

5 stars
I made these for my family yesterday morning and everyone loved it! My family had eaten all of them by the time I went for seconds! I’m going to make them again today or tomorrow, and was wondering if I made a double batch if I could freeze some of the batter? These are definitely a new family favorite. Thank you!

We’ve never tried freezing the batter- we usually bake the muffins before freezing. So glad your family loved them!

I put apples through the juicer and then used this recipe with the scraps! I added a scoop of protein powder and a half cup of yogurt. I also subbed some almond flour just to use it up! So yummy!