Name: Low Calorie Greek Yogurt Apple Muffins
Prep time: 15 min
Cook time: 25 min
Total time: 40 min
Ingredients: 1 Apple (cored and peeled); 1 cup Greek Yogurt (low fat); 1/2 cup Applesauce (unsweetened); 1 Egg; 1 teaspoon Vanilla Extract; 1 cup Gluten Free Baking Flour; 3/4 cup Gluten Free Rolled Oats; 1/4 cup Coconut Sugar; 1 1/2 teaspoons Baking Powder; 1/2 teaspoon Baking Soda; 1 teaspoon Cinnamon; 1/4 teaspoon Salt

This post contains affiliate links. As an Amazon associate I earn qualifying purchases. Click here for more about this policy.

Jump to Recipe Print Recipe

Low Calorie Greek Yogurt Apple Muffins are higher protein, healthy and easy to bake! Made with oats, cinnamon, yogurt and flour they make a yummy fall treat! Gluten Free + Low Calorie

Fall recipes are the best recipes! I eat apple and pumpkin everything year round, but there's something about fall that makes you want to eat it more!

Healthy apple crisp, apple pancakes and bacon apple Brussels sprouts are staples in my home.

These healthy Greek Yogurt apple muffins will now be added to my list of fall staples too!

Are Apple Muffins Healthy?

These apple muffins are a healthier version as they are higher protein, higher fiber, have whole grains and are low in sugar. They're nutritionally balanced making them a better for you treat!

They're also lower in calorie and gluten free. Here's more details on why they're a better muffin option for you.

What Makes This Low Calorie Greek Yogurt Apple Muffin Recipe Healthy?

Higher Protein - Each muffins has 4 grams of protein. I cannot stress enough the importance of adequate protein intakes. My clients are always really deficient in this important nutrient so sneaky it into recipes like this one is key!
Low Sugar - There is very little added sugar in this recipe only 1/2 cup across 12 muffins which is very low. The remaining sugar is coming from natural sources which is what we want.
Low Calorie - Only 97 calories per muffin!
Everyday Ingredients - Most of these ingredients are likely staples you have already in your home!
Gluten Free - I'm gluten free for my Hashimoto's disease. See the substitutions section if you do not need to be gluten free.

healthy apple muffin ingredients with Greek Yogurt

Ingredients For Low Calorie Apple Muffins With Greek Yogurt

These healthy apple muffins are made with everyday ingredients. I'm sure you have most of them already on hand!

Apple
Greek Yogurt
Applesauce
Egg
Vanilla Extract
Gluten Free Baking Flour (see substitutions below)
Gluten Free Rolled Oats
Baking Powder, Baking Soda
Cinnamon, Salt
Coconut Sugar

You will also need a muffin tin, cooking spray or muffin liners, a mixing bowl and a tool to grate the apple with.

You can find substitutions for ingredients in the substitutions section below!

steps to make healthy apple muffins with Greek Yogurt

How To Make Low Calorie Greek Yogurt Apple Muffins

Making healthy apple muffins is easy! Here's the steps to make healthy apple muffins.

Step One - Preheat the oven to 350 F and prepare a muffin tin.

Step Two - Combine the dry ingredients in a large mixing bowl.

Step Three - Combine the wet ingredients in another mixing bowl. Grate the apple then fold it in.

Step Four - Add the wet ingredients to the dry ingredients and mix together. Scoop the batter and fill each cavity 3/4 of the way full.

Step Five - Bake the muffins 22 minutes or until a toothpick can be removed clean. Remove from the oven and cool 10-15 minutes before removing from the pan. Enjoy!

What Apples Are Best For Making Muffins?

Any apple will work for baking apple muffins, but I recommend using one that you enjoy eating and that is naturally sweet. Some apples are sweeter than other apples so it's important to consider that to get the best muffins.

I used Honey Crisp for this recipe as I find a they taste best, but they are expensive and not always accessible for everyone. Use the apple variety that makes sense for you!

How To Keep Moisture In Muffins

The secret to keeping muffins moist is having the right balance of ingredients. The Greek Yogurt in this recipe makes these low calorie apple muffins creamy and moist.

The right measurements of flour will also impact the moisture of your muffins. It's important to measure properly when baking otherwise you will end up with too much flour and dry muffins.

Should Muffin Batter Be Refrigerated Before Baking?

Chilling muffin batter overnight is one the best secrets to making amazing muffins. It will make them tender and taller! I know it's not realistic for everyone to refrigerate their batter overnight prior to baking so it's not required.

Why Are My Muffins Flat On Top?

Flat muffins are a result of underbaking or not measuring the baking flour or baking soda properly. Also, old baking flour and baking soda will do this.

How To Make Apple Muffins Gluten Free?

This low calorie apple muffin recipe is made with gluten free ingredients. If you do not need to be gluten free, see the substitutions section below!

How To Store Low Calorie Apple Muffins

Storing - Skinny apple muffins can be stored in the refrigerator up to 7 days in a sealed container. I do not recommend keeping them at room temperature due to the yogurt.
Freezing - You can freeze these muffins up to 3 months. I recommend placing in a plastic storage container then defrosting them the night before you want to eat them in the refrigerator.

Substitutions For Healthy Greek Yogurt Apple Muffins

Here's the substitutions I recommend for making skinny apple muffins. Remember when you substitute ingredients it will change the nutritional data you see below.

Applesauce - While I don't recommend substituting the applesauce (the muffins won't be as moist and flavorful), you could substitute with pumpkin or oil.
Apples - Any apple variety will work. You could also substitute with pears.
Greek Yogurt - I do not recommend substituting this ingredient as it is the ingredient that makes these muffins creamy. For a dairy free yogurt, I recommend this Kite Hill version as it is higher in protein than other dairy free brands and tastes great.
Egg Free - I have not tried making these muffins egg free so I cannot guarantee results. But you could try a flax egg (1 tablespoon flax meal mixed with 2 tablespoons of water) or an egg replacer like this one.
Gluten Free Baking Flour - You can use whole wheat flour if you're not gluten free. For an almond flour version, see this Paleo apple muffin recipe. Coconut flour will not work.
Gluten Free Rolled Oats - You can use regular oats. I don't recommend using quick oats as it will change the texture.
Coconut Sugar - Any sugar may be substituted.
Paleo - This apple muffin recipe is Paleo friendly.

More Healthy Muffin Recipes

About Megan

Megan is a certified nutrition practitioner, author, freelance food photographer and fitness instructor living in Phoenix, Arizona. On her blog, Skinny Fitalicious she shares EASY, gluten free recipes for weight loss. Follow Megan on Facebook, Twitter, Pinterest and Instagram for the latest updates.

Low Calorie Greek Yogurt Apple Muffins {Low Cal, GF}