Healthy Cinnamon Apple Muffins

by Erin @ Food Doodles on June 18, 2020

These healthy cinnamon apple muffins are made healthier with whole wheat flour, olive oil (or another oil of choice), and less sweetener than a typical muffin! Despite that, they’re so moist and flavorful. They can also be made gluten-free and dairy-free.

I’m super excited about these muffins! If you prefer cupcakes, check out my Applesauce Cupcakes with Cream Cheese Frosting.


These apple muffins don’t taste at all healthy and have the most amazing texture. Super light, fluffy and far, far from dense or cardboardy, like some other whole wheat or gluten-free recipes.

I’ve been making the whole wheat version for about 10 years. You can use whole wheat flour, white whole wheat flour, or whole spelt flour.

You can alternatively use all-purpose flour. Each version tastes the same.

And yesterday, I finally tried it out with my favorite gluten-free baking flour and it worked perfectly! I’ve used that flour in so many recipes, like these Chocolate Orange Scones and Gluten-free Chocolate Cupcakes with great success.

I should say that the gluten-free baking flour is equivalent to all-purpose flour in terms of health. So it’s not exactly healthy but even using that or AP flour, these cinnamon apple muffins are still healthier than your average apple muffin with butter, white sugar, etc.

You can make these honey-sweetened apple muffins plain – with no topping at all – or with a sprinkle of cinnamon sugar or with streusel on top.

Obviously, I chose streusel. The muffins really don’t need it but I’m a streusel fiend, so…

The streusel recipe makes quite a bit. No dinky sprinklings of streusel here!

By the way, I really do not like the above photo but had to include it to try to show you how fluffy these are. But it doesn’t do these muffins justice!

If you make them plain, then the muffins are totally honey-sweetened. I used brown sugar for the topping. Coconut sugar also work. It’s hard to make streusel with honey. πŸ˜‰

No matter which version you make, you can taste the olive oil in the batter (like in my Healthy Chocolate Cake and Healthy Applesauce Muffins). And just like in those other recipes, it disappears post-baking!

For the gluten-free and all-purpose flour versions, you can taste the olive oil a little even after the muffins have been baked. They need to cool completely and then the taste somehow disappears. 

I used extra-virgin olive oil so if you use a lighter olive oil, the muffins likely will be olive-oil-taste-free straight from the oven. But I thought they still tasted amazing, even with the slight olive oil taste!

It’s just a warning for the people who want to be sure they can’t taste it at all.

The spices – cinnamon, nutmeg and allspice – do a great job of covering up the whole wheat and olive oil tastes so I don’t recommend skipping them.

You can skip the allspice but cinnamon and nutmeg are important. If you love spiced goodies, check out my Spiced Apple Cranberry Smoothie and Chai Spiced Apple Butter Crumble Bars.

If you don’t want to use olive oil, you can use whatever oil you’d like. If using coconut oil, I recommend using refined coconut oil, unless you want some coconut taste. I haven’t tried unrefined coconut oil so it could be that the spices cover up the coconut taste, but I’m not too hopeful about that.

Instead of yogurt, I’ve used buttermilk a few times. Vanilla yogurt would work, too. The muffins will just be a little sweeter.

To make them dairy-free, you can use whatever type of dairy-free yogurt you’d like. I made my last batch with coconut milk yogurt, expecting a slight coconut taste, but they didn’t taste at all coconutty.

You can also make homemade dairy-free buttermilk. Add 3/4 teaspoon of lemon juice, white vinegar or apple cider vinegar to a 1/4-cup measuring cup. Fill with dairy-free milk and let sit for 5 minutes.

Strangely enough, the whole wheat apple muffins are moister on the second day, but they’re still awesome straight from the oven. I do love it when things turn out better on the second day!

If I’m having people over for breakfast, I make it hard on myself and get up super early because I want the baked goods to be as fresh as possible. That’s definitely not necessary with these! 

The muffins you see in the photos above are the gluten-free version. If you make the whole wheat ones, the muffins are darker in color. Here’s an old photo of the whole wheat version (this recipe used to be over on my other blog and that’s why it’s watermarked as

The streusel also looks different because the gluten-free version has a different streusel recipe. I find streusel difficult to convert to gluten-free so I just used a recipe that I know that works. 

After I took these photos, I picked the streusel off all the muffins and was so happy. πŸ˜€ I do the same with this Roasted Banana Almond Butter Streusel Bread. It’s really good stuff. 

If you love apples and cinnamon as much as I do, try this great looking apple cinnamon oatmeal for an even healthier option.

Whole Wheat Apple Muffins

Questions about these healthy cinnamon apple muffins?

Can I use a different flour?

I’ve tried these muffins with “only” the 4 flours listed. That’s all I can guarantee to work. You could probably use a different gluten-free baking blend that’s meant as a 1-to-1 sub for all-purpose flour but they probably won’t have such an awesome texture. With the one listed, they’re not at all gummy, gritty or anything. They’re just perfect!

Can I omit the spices?

I really recommend using at least the cinnamon and nutmeg! If you don’t want to use nutmeg, increase the cinnamon to 2 teaspoons. You can omit the allspice if you want.

How can I replace the egg?

I unfortunately didn’t think to make these with an egg replacement. I’ve always had issues with egg subs in muffins and cakes. As these healthy cinnamon apple muffins only call for 1 egg, I think a chia or flax egg would probably work, but I haven’t tried it.

Can I use something other than honey?

Maple syrup would very likely work (but I haven’t tried it). If you used a granulated sugar, you’d have to add a little more liquid but without trying it myself, I can’t say how much you’d need to add.

I really recommend honey or maple syrup!

Can I reduce the sweetener?

You could probably get away with 1/4 cup instead of 1/3 cup. They’ll be a little less moist but I still think they’d be good.

Can I use a different oil?

I think any oil would work. I’ve used extra-virgin olive oil, canola oil and refined coconut oil without issue. Butter would reduce the amount of fat in the recipe, though (as it’s 80-82% fat versus 100%) so I don’t recommend that unless you’re okay with the muffins being a little drier. 

Can I use something other than yogurt or buttermilk?

You can make homemade buttermilk (with dairy or dairy-free milk) but you need some kind of acidic ingredient here for the baking soda to do its work. So yes, please use yogurt or buttermilk!

Can I use a different fruit / omit the apples?

Blueberries or raspberries would probably be great. I’m hesitant to recommend other fruit because they’re already very watery and these muffins are already super moist. If you want something different, try my Spelt and Oat Pear Muffins or Apple Cranberry Bran Muffins.

Can I use applesauce / grated apples?

You’d need to rework the whole recipe to include applesauce, so no to applesauce. I’m not sure about grated apples because again, you’d be adding a bit of liquid to the recipe. I’m 50 / 50 on that one.

Can I use something other than butter in the wheat version streusel?

That’s the only way I’ve tried it. If you want to use coconut oil, you’d probably need to use a little less. I’m guessing half a teaspoon less, so 1 tablespoon + 2 teaspoons for a total of 23 grams of coconut oil. But it’s just a guess!

Can I use something other than coconut oil in the gluten-free streusel?

That’s the only way I’ve tried it. If you want to use butter, you’d probably need to use a little more. I’m guessing an extra teaspoon for a total of 51 grams of butter. But it’s just a guess!

Any other questions? I think I have every ingredient covered. πŸ˜€ If you try out these healthy cinnamon apple muffins, I’d love to hear what you think!

Healthy Cinnamon Apple Muffins
Prep Time
20 mins
Cook Time
17 mins
Course: Breakfast
Servings: 9 muffins
  • 1 cup (125 grams) whole spelt, whole wheat flour, all-purpose flour or for a gluten-free version, use 1 cup (138 grams) Bob's Red Mill Gluten-free 1-to-1 Baking Flour
  • 3/4 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1/4 teaspoon salt
  • 1 teaspoon cinnamon
  • 1/2 teaspoon nutmeg
  • 1/4 teaspoon allspice, optional
  • 1 large (50 grams, out of shell) egg
  • 1/3 cup (106 grams) honey
  • 1/4 cup + 2 tablespoons (90 ml) olive oil* or another neutral-tasting oil (if you want to use coconut oil, use refined for no coconut taste)
  • 1 teaspoon vanilla extract
  • 1/4 cup (60ml) plain yogurt or buttermilk (use dairy-free yogurt or homemade dairy-free buttermilk** for a dairy-free version)
  • 1 cup (120 grams) diced apple, preferably from baking apples like Granny Smiths (I needed one medium / large apple and diced chunks about 1/4" in size)
  • 1/3 cup (45 grams) whole spelt, whole wheat flour or all-purpose flour
  • 1/2 cup (100 grams) brown sugar or coconut sugar
  • 2 tablespoons (28 grams) melted unsalted butter
  • 2 teaspoons cinnamon
  • 1/8 teaspoon salt
  • 1/2 cup (69 grams) Bob's Red Mill Gluten-free 1-to-1 Baking Flour
  • 7 tablespoons (88 grams) brown sugar or coconut sugar
  • 3 tablespoons + 1 teaspoon (47 grams) melted coconut oil
  • 2 teaspoons cinnamon
  • 1/8 teaspoon salt
  1. Mix the streusel ingredients in a small bowl until well combined. ***

  2. Preheat the oven to 350Β°F / 175Β°C. Line a muffin tin with 9 muffin liners.

  3. In a medium bowl, whisk together the dry ingredients (flour through salt).

  4. In another bowl, mix the wet ingredients (egg through yogurt).

  5. Add the flour mix to the wet mix. It just needs to be combined, so be careful not to overmix.

  6. Then fold in the apples, being careful not to overmix.

  7. Fill the liners with the batter, filling them about 2/3 full.

  8. Divide the streusel between the muffins. If you like being exact, that's 20 grams per muffin for the wheat version and 23 grams for the GF version. It's a little more than a tablespoon.

  9. Bake for about 15 – 17 minutes or until a toothpick comes out clean. I needed 15 for the wheat version and 17 minutes for the GF version. But all ovens vary so have an eye on them.

  10. Let the muffins cool for 5 minutes and then turn out onto a wire rack to cool.
  11. When the muffins are completely cooled, place them in an airtight container and store at room temperature for up to 4 days. Anything past that, store in the refrigerator.
Recipe Notes

Please read the post for more tips and answers to the most common questions!

* If you want to make the gluten-free version and eat them straight from the oven and have no olive oil taste, you'll likely want to use a lighter olive oil and not extra-virgin. See post for more notes on olive oil type.Β 

** To make dairy-free buttermilk, add 3/4 teaspoon of lemon juice, white vinegar or apple cider vinegar to a 1/4-cup measuring cup. Fill with dairy-free milk and let sit for 5 minutes.

*** If you don’t want to make the streusel, add some cinnamon sugar (1 tablespoon raw sugar or granulated sugar + 1 teaspoon cinnamon) to the top of the muffins. It adds a wonderful crust and a little extra sweetness.

Leave a Comment

{ 27 comments… read them below or add one }

1 Kimberly December 18, 2021 at 12:24

I’m wondering if you could sub applesauce for some or all of the oil?


2 Erin @ Food Doodles December 19, 2021 at 06:43

I haven’t tried it but you could try half oil, half applesauce.


3 Ashley May 2, 2021 at 13:43

If anyone asks..”Just egg” egg replacer works great…kid-approved πŸ™‚ Just 3 tablespoons of the egg replacer and they came out great!


4 Erin @ Food Doodles May 3, 2021 at 16:00

I’m so glad to hear that! Thanks a bunch for the tip. πŸ™‚


5 Julia March 29, 2021 at 19:29

I will be making these! Do you think i can use oat flour for the streusel and/or actual muffin?


6 Erin @ Food Doodles March 30, 2021 at 09:06

I hope you’ll enjoy them! And I don’t think that’d work. Oat flour is so much more absorbent than other types of flour. Sorry about that!


7 Meghan November 9, 2020 at 03:02

These are FANTASTIC! I’ve tried several muffin recipes since going gluten-free, and they’ve all been disgusting. Not these! I am VERY picky (literally ask any of my friends), and I would eat these even if I wasn’t gluten free! I even made them without the streusel topping, because I cannot eat the sugars listed in the streusel recipes. They are still delicious! I only made a single batch because I’ve been so disappointed by so many other recipes, but as soon as I tasted these, I wished I had made a triple! It was hard not to eat them ALL straight from the oven…. FINALLY something that isn’t just “good, for a gluten free muffin,” but actually, truly delicious!!


8 Barb November 4, 2020 at 20:58

These are SO good! I did cut the sweetener to 1/4 c. and left off the streusel to make them healthier, but they were excellent! The flavor combination of the spices and apples hit the nail on the head, and the muffins were nice and moist without being soggy, even though I made the reduction in the sweetener. I’m embarrassed to say that my hubby and I managed to eat eight of them between us at dinner, and the last one disappeared shortly thereafter. Just printed off the recipe so I can do this again!


9 Coralia Varga June 30, 2020 at 09:59

These are husband and friends approved. They tasted absolutely divine. We ate them for breakfast and wow!


10 Erin @ Food Doodles July 4, 2020 at 12:48

Yay! I’m glad to hear that you enjoyed them. πŸ™‚ Thanks for your feedback!


11 Kathryn June 29, 2020 at 15:58

I love the combination and flavor of cinnamon and apples! Muffins are always a go-to recipe so I can’t wait to add this to my list to make this weekend for the 4th of July! Thanks πŸ™‚


12 Erin @ Food Doodles July 4, 2020 at 12:49

I hope that they’ll make it to the top of your list! πŸ˜‰ I’d love to hear how they come out!


13 Mikayla June 29, 2020 at 00:20

I make a lot of healthy muffins with a toddler in the house and these were a hit! Soft and fluffy, and loved the spices with the apple flavor. Great recipe!


14 Erin @ Food Doodles July 4, 2020 at 12:50

Thank you! I’m so happy that they were a hit. Thanks a bunch for your comment!


15 Pam Greer June 27, 2020 at 20:35

These are so light and fluffy and I love that they are healthy! We like them for dessert, a snack or even breakfast!


16 Erin @ Food Doodles July 4, 2020 at 12:50

I’m glad to hear that! Thanks for the feedback. πŸ™‚


17 Denise June 27, 2020 at 17:56

This is a perfect muffin! The flavors are lovely, so good any time of year for breakfast or a snack!


18 Erin @ Food Doodles July 4, 2020 at 12:50

I agree. πŸ˜‰ Thank you!


19 Tammy June 26, 2020 at 23:59

Oh my goodness these look so amazing! So moist inside and I love streusel! It’s such a treat having a muffin in the morn with my coffee ^_^


20 Kari June 26, 2020 at 03:26

I love apple cinnamon flavour combos and this recipe looks so moist, even while it’s healthy so I will be printing and making this for the lunchbox!


21 Erin @ Food Doodles July 4, 2020 at 12:59

I hope your kid will enjoy them as much as we do!


22 Eva June 23, 2020 at 13:50

Wait – olive oil in apple muffins? I had never thought about that and I would be one not to mind the flavour of olive oil! On top of all the spices and the flavour that the apples also give, olive oil sounds like the perfect hint to finish off a great combination of flavours! I definitely have to give this recipe a try, as I love the idea of using olive oil in fruit muffins.


23 Amanda June 23, 2020 at 10:59

These muffins were perfect! They were so moist, and I love that they weren’t too sweet. Plus, they were super simple to make!


24 Erin @ Food Doodles June 24, 2020 at 20:15

Woohoo! I’m so happy that you thought that they were perfect and simple to make. I definitely don’t like fussy. πŸ˜‰ Thanks a bunch for your comment!


25 Linda June 23, 2020 at 10:11

I love apple muffins and all those spices were the perfect addition. And, of course, I had to try the gluten free version for my daughter and they came out just like you said, moist and spicy. I’m bringing them to her today and know she’ll devour them.


26 Erin @ Food Doodles June 24, 2020 at 20:13

Oh, yay! I’m so glad to hear that you enjoyed them and that you found them how they were described. I hope your daughter will like them, too. πŸ™‚ Thanks a ton for your feedback!


27 Charlotte Moore June 18, 2020 at 16:05

Oh yum! My kind of muffins. Love whole wheat, or spelt, apples, and cinnamon. I don’t care for cloves so I just leave it out of recipes.


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