These Healthy Apple Muffins are the perfect Fall breakfast, treat, or snack. Made with only real food ingredients, they are gluten free, dairy free, and refined sugar free, but have all the warm and comforting flavors of the season! This post contains affiliate links for products I’m obsessed with.
This is a sponsored post on behalf of Bob’s Red Mill. As always, all opinions are 100% mine. Thank you for supporting the brands that help make Confessions of a Fit Foodie possible.
Healthy Apple Muffins
I took a quick poll on social recently asking which is the favorite Fall flavor: pumpkin or apple.
And you know what?
I was shocked by how many apple fans are out there. I hear so much about everyone’s love for all things pumpkin, but wow…many of you want more apple recipes and I am here for it! To be fair, I am here for all the recipes and all the flavors, but anywho – let’s get on with the show and talk about these unbelievably yummy apple muffins! 😍
Muffin recipes are super popular on the blog – we have Healthy Banana Oatmeal Blender Muffins, Healthy Carrot Cake Muffins, Gluten Free Chocolate Chip Zucchini Muffins, Gluten Free Blueberry Muffins and now these healthy gluten free apple muffins are joining the club! My kids LOVED these muffins and I can’t wait for you all to try them!
Dry Ingredients for Healthy Apple Muffins:
- Bob’s Red Mill Gluten Free 1-1 Baking Flour: I used my favorite baking flour in these muffins so they are safe for my gluten free kiddo, and I know I can trust the texture to be spot on perfect. After trying many gluten free flours, Bob’s is the brand I go back to again and again.
- Cinnamon: because apples + cinnamon are everything I love about Fall.
- Pumpkin pie spice: this is optional, but I love the little extra pop of flavor it brings to these muffins.
- Baking soda and baking powder: I use both to get that perfect rise. Tip: be sure you replace these every few months for best results when baking.
- Salt: to help bring out the sweetness in the muffins.
- Raw sugar (with an optional dash of cinnamon): a tiny bit of raw sugar added to the tops of these muffins elevate them oh-so-much…think store bought bakery style according to my daughter (this is sadly her highest compliment 😂). I also added a dash of cinnamon for apple cider donut vibes 😍.
And of course you need Apples!
I used my favorite Honey Crisp apples, cut into small chunks…I love getting a little bite of apple in my muffins – like a mini burst of apple pie. If you have picky kiddos, you can grate your apples into fine pieces, but both my daughter and I prefer the chunks!
Tip: If you ever added fruit to your muffins and it sank to the bottom, mix your fruit into and coat with the dry ingredients first, instead of folding your fruit into the batter. It will definitely help those chunks stay put!
Wet Ingredients for Healthy Apple Muffins
Here’s whatcha need to add to that flour mixture:
- Oil: you can use melted coconut oil, avocado oil, or extra virgin olive oil in this recipe.
- Maple syrup: I prefer maple syrup to honey in my baked goods, but it can be swapped in a pinch.
- Pure vanilla extract: a muffin ingredient staple!
- Eggs: I haven’t tried it, but I think flax eggs could work if you are looking for a vegan option.
- Unsweetened applesauce: feel free to use homemade or store bought – they both work great.
How to Make Healthy Apple Muffins
- Preheat oven to 425 and prep your muffin tin with liners – I LOVE the parchment kind because you know nothing is gonna stick.
- In a medium sized bowl, mix up those wet ingredients.
- In a larger mixing bowl, mix flour, cinnamon, baking soda, baking powder, and salt. Fold apples into dry mixture and coat evenly. Stir wet ingredients into the dry and incorporate well.
- Divide muffin batter into prepared cupcake tins. Sprinkle tops of muffins with raw sugar.
- Cook for 14-16 minutes or until a toothpick comes out clean. Inhale!
What kind of Apples are best for baking?
Any apples will do in this recipe, but I would look for a sweet, firm apple like:
- Honey Crisp
- Pink Lady
Can I freeze these Gluten Free Apple muffins?
Yes! I highly recommend you make a double batch of these muffins and freeze some for when the cravings strike, or when you need a quick breakfast. Just freeze in an air tight container, stasher bag, or ziplock bag, then thaw on the counter or in the fridge. You can also thaw in the microwave if you can’t wait!
What kind of flour can I sub for gluten free flour?
If you aren’t gluten-free, you can sub Bob’s Red Mill Whole Wheat Flour in this recipe with a perfect 1:1 swap. These muffins also works great with Oat Flour, which will add extra fiber, too!
More Yummy + Healthy Apple Recipes for Fall –
Instant Pot Apple Crisp | Gluten-free Apple Crisp
Caramel Apple Dip | Caramel Apple Nachos
Gluten Free Stuffing with Sausage + Apple
Instant Pot Apple Butter | The Foodie and The Fix
Thank you Bob’s Red Mill for sponsoring this post. It means so much to me to work with brands that I love and use in my kitchen every day!
Healthy Apple Muffins [Gluten Free + Dairy Free]
- ¼ cup melted coconut oil, avocado oil, or extra virgin olive oil (I used avocado oil)
- ½ cup maple syrup ⅓ cup for WW
- 2 eggs room temp
- 1 cup unsweetened applesauce
- 1 tsp vanilla
- 1 ¾ cup of Bob’s red mill 1-1 gluten free baking flour
- 2 tsp cinnamon
- ¼ tsp pumpkin pie spice can sub all spice or omit
- 1 tsp baking soda
- 1 tsp baking powder
- ½ tsp salt
- 1 ½ cups finely diced apples (¼ inch chunks or less) no need to peel - I LOVE honeycrisp for these
- 1 tablespoon raw sugar with optional dash of cinnamon
- Preheat oven to 425. Line a 12 space muffin tin with parchment liners.
- In a medium sized bowl, beat oil and maple syrup together, then beat in eggs. Add in applesauce and vanilla and set aside.
- In a larger mixing bowl, mix flour, cinnamon, baking soda, baking powder, and salt.
- Fold apples into dry mixture and coat evenly. Stir wet ingredients into the dry and incorporate well.
- Divide muffin batter into prepared cupcake tins. Sprinkle tops of muffins with raw sugar.
- Cook for 14-16 minutes or until a toothpick comes out clean.
Excited to make these! Can you sub whole wheat flour instead if you’re not gluten free?
Is this gut protocol approved
But if you subbed plain, GF rolled oats and made your own oat flour instead of using the 1:1 flour AND left off the raw sugar on the top, you could make it work. Even with leaving the raw sugar out, one muffin would be 8g of your allotted 10g of sugar for the day so you would have to decide if that is worth it to you!
Jonna Rose Ball says
These look amazing! Are these in a regular size muffin tin or a jumbo? The liners you link to are for the larger size but there isn’t anything in the write-up to indicate…thank you!
Hi! Regular muffin size for these. Thank you so much for letting us know the wrong size parchment liners were linked! All fixed now!
One of my absolute favorite things to bake, especially in the Fall! I’ve made with both the WW and GF flours and winter is great! Love the amount of cinnamon in them! I recommend using the Kirkland brand from Costco!
Patricia Milker says
These are just freaking amazing!!! So much flavor, pretty easy to make, and just dang delicious!!! I absolutely love that the recipe falls into the clean eating plan I follow too!! My jeans and my tastebuds say thank you!!!❤️
Thank you Patricia! You are the best cheerleader!
Lindy Beshore says
These muffins are a must have fall treat! Perfectly sweet, bursting with apple flavor and spices. I ate mine with a smear of PB because why not!! I love that they fit perfectly into my nutrition plan too. Another amazing recipe!
PB is my love language so I’m totally on board with that addition! lol!
DELICIOUS! I was impressed with how yummy they tasted and not like a “diet” muffin. Used the instant pot applesauce recipe to make the applesauce and used that in the recipe. I however did not add the raw sugar on top and I’m glad I didn’t, because they are perfectly sweet. Not too sweet at all and the right amount of flavor. Such a perfect fall breakfast. I love how it doesn’t make me feel full or bloated, but satisfied! Definitely going to make them again to share as a snack 🙂
These are delicious. Honestly, the best gluten free quick bread I’ve made. my local store didn’t have Bob’s red mill, but had Sunset brand. They came out great, not gummy like has happened with other GF recipes. I used homemade applesauce and nutmeg and dashes of clove and ginger for the pumpkin pie spice. I will be putting these in my rotation! thanks!
Thank you Katy! These are huge compliments!
Susan Zepeda says
Oops, forgot the rating…definitely a save for my recipe book at 5 stars 🙂
lol! Thank you soo much Susan!
Susan Zepeda says
These are perfect for a fall breakfast- I’ve been enjoying them all week. Thank you for a recipe that even my picky 7 year old loves.
Yay for winning over picky eaters! Thank you for your comment!
Jenni Monaco says
Wow! These are fantastic and a very simple recipe to follow. Great flavor using gala apples. Also, why have I never tried parchment liners before? Not a single crumb stuck to the liners!! Thanks for another great recipe!!
Parchment liners for the win – woohoo! Thank you Jenni!
These are absolutely delicious and so moist!! They’re just what I was looking for to add to breakfast and send off to school with my girls in their lunch boxes. Definitely will be making again!
I love the lunchbox idea Rita!
I made these today and they were so good!!! I used homemade applesauce that we had made from apple picking. I didn’t use the pumpkin pie spice because I didn’t think everyone would like it . The kiddos couldn’t get enough of them!
This is great feedback, thank you Jean! I love that you used homemade applesauce too!
Melody McGaha says
These were delicious and easy to make! My very picky kids approved and asked for seconds. That’s not always the case with things that are healthier!
This is a huge win! Thank you for your comment!
These were delicious! I actually forgot the raw sugar on the top but can’t wait to make them again. ☺️ I have shared the recipe with several friends today.
Nicole, thank you for sharing the recipe! That’s a huge compliment!
Whitney Lawson says
These are amazing! My husband who is super picky even enjoyed these. Will def be making these again!!
So glad you and your husband loved the muffins. Thank you for the comment and for rating the recipe!
anyone try this using almond flour?
Almond flour will likely end up being too dense for these. Oat flour or whole wheat are good substitutes for the gluten free flour blend!
Diane Gaw says
I just made these to take to a girls’ weekend. They are amazing! I have fresh picked apples we picked ourselves at Solebury Orchards. I used whole wheat flour and coconut oil. And I did throw in the Pumpkin Pie Spice! My daughter and I split one as a taste test and she gave me a thumbs up. Thank you, Nancylynn! I’ve lost 5 pounds in about a month and am loving your recipes!
I want someone like you on my girls weekends! Yum! Keep up the good work, Diane!
What a fantastic recipe – I’m always looking for healthy, gluten and dairy free recipes… I ate two right away…. Just yummy!
Ahhh Kelley, thank you so much! SO glad you liked them!
Just made these for the 3rd time in a row with positive feedback! This truly is a no fail recipe. Thank you so much for your commitment to getting us recipe challenged folk. You are a topic of conversation in my circle of friends and family, I will follow you around the kitchen all day long! Thanks again-Elizabeth
Absolutely love this recipe, I used whole wheat flour and topped with some chopped nuts,so delicious! Thanks
AHH thank you!
can I substitute the maple syrup for sugar?
I haven’t tested it with sugar, but let us know if you try it!
These are soo delicious!! My son and I just devoured a couple!! Looking forward to breakfast all week!!
Woohoo! It’s easy to sneak a couple right out of the oven – been there! lol!
These were so simple to make and absolutely delicious!
You made my day, Sara! Thank you for rating and reviewing! 💕💕💕
I made these with whole wheat flour and they turned out great! I did need to bake them for about 20 minutes to get the centers cooked, but totally worth it!
Great info, thank you!! So glad you loved them!
I made those yesterday and ate TWO before I even knew what I was doing!! Needless to say, someone didn’t get to have a tortilla for taco night last night! 😉 I had to eat my taco as a salad cuz I chose to eat my “tortilla” in the form of apple muffins! They’re AMAZING and it was SO worth it!! NancyLynn, you always fill my heart and tummy with so much joy!
Awww, I love this, Carrie! Thanks for trying these and taking the time to write such a great review 💕💕💕💕