Healthy Apple Muffins with Greek Yogurt

Warm up your mornings with these Healthy Apple Muffins, with added protein! Fluffy, easy to bake, and made with wholesome ingredients like fresh apples, these apple bites are a feel-good treat for any day of the week—especially when you are looking for comforting fall flavor.

As soon as fall hits, I dive into apple recipes, and these healthy apple muffins quickly become a staple in my breakfast routine. Simple, wholesome, and perfectly balanced, these breakfast bites are low-calorie, high-protein, high-fiber, and low in sugar—making them the ideal choice to fuel your morning.

Baked with fresh apples, creamy Greek yogurt, wholesome eggs, warm cinnamon, and gluten-free flour and oats, they are easy to grab, satisfy your sweet cravings, and keep you full until your next meal.

Craving more fall-friendly apple recipes? Try this gluten free apple crisp recipe and apple oat pancakes next!

Why You'll Love This Recipe

• Higher in Protein: Protein is crucial for keeping us full and satisfied, so sneaking it into this healthy apple recipe is a great way to make sure my weight loss clients and you are getting enough in a delicious, easy-to-enjoy form!
• Low in Sugar: With just 1/2 cup of added sugar for the entire batch of 12, they are naturally sweetened by the apples, making them a low-sugar, healthier option compared to many other store-bought, baked goods.
• Simple, Everyday Ingredients: Made with gluten-free staples you likely already have at home, these muffins come together easily with ingredients that are both wholesome and accessible.

Healthy Apple Muffins Ingredients

• Apple: Adds moisture, fiber, texture, and that signature apple flavor. Any apple variety works, or you can substitute pears for a different fruity spin. Use extra apples to make these Brussels sprouts with apples too!
• Greek Yogurt: Provides tanginess and protein while reducing the need for added fat. It’s the yogurt that gives them their creamy texture, so I don’t recommend substituting it. See below for a dairy-free option.
• Applesauce: Acts as a moisture agent and fat substitute, keeping the muffins tender and moist. If you must substitute, consider using pumpkin puree or a mild oil, but note that applesauce keeps the flavor and texture optimal.
• Egg: Binds the ingredients together and adds richness. While I haven’t tested egg-free options, a flax egg (1 tbsp flax meal + 2 tbsp water) or egg replacer could work as alternatives.
• Gluten Free Rolled Oats: Contribute fiber, nutrients, and a pleasant chewiness. While you can use regular oats, I recommend avoiding quick oats, as they’ll alter the texture and may not turn out as well.

See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.

Variations & Dietary Modifications

• Nut Medley: Add crunch and healthy fats by incorporating your favorite nuts, such as chopped walnuts, almonds, or pistachios.
• A Touch of Chocolate: For a hint of sweetness, fold in a moderate amount of dark chocolate chips to maintain a lower sugar content.
• Dairy-Free Option: If you need to make dairy free apple muffins, I recommend using a dairy-free yogurt like Kite Hill. It’s higher in protein compared to other dairy-free brands and has a great flavor.
• Flour Alternatives: This recipe is made with gluten-free ingredients, but you can use whole wheat flour if you're not gluten-free. Note that coconut flour won’t work as a substitute.
• Make it Paleo: To make these healthy apple cinnamon muffins Paleo-friendly, use almond flour in place of the gluten-free flour blend or try almond flour apple muffins instead!

How To Make Healthy Apple Muffins

Making healthy apple muffins is easy and quick! Preheat your oven to 350°F, grab a muffin tin, cooking spray or liners, a mixing bowl, and a grater to start. Then, grate the apple, gather the other ingredients, and follow these 4 simple steps.

Step 1: Combine the Dry. In a large mixing bowl, mix together the flour, oats, sugar, baking powder, baking soda, cinnamon and salt, until well combined.

Step 2: Stir in the Wet. Fold in the grated apple, egg, applesauce, yogurt and vanilla to the dry ingredient mixture.

Step 3: Scoop the Batter. Spoon the batter into each muffin cavity of the greased tin, filling each cavity only 3/4 of the way.

Step 4: Bake and Enjoy. Bake at 350°F for 22-25 minutes or until a toothpick inserted comes out clean. Cool for 10 minutes, transfer them to a wire rack, and enjoy!

Take them on the go with a comforting, fall-flavored smoothie like this carrot smoothie or pumpkin smoothie recipe.

Expert Tips

• Stir by Hand: Stirring the batter by hand prevents over-mixing, which can lead to dense muffins. Keeping it light and fluffy is the key!
• Correctly Measure Flour: For the best results, spoon the flour into your measuring cup and level it off with a knife. This prevents packing the flour, which can make them dry and heavy.
• Storage: These easy healthy apple muffins can be stored in the refrigerator for up to 7 days in an airtight container. I don't recommend keeping them at room temperature due to the yogurt. You can also freeze them for up to 3 months. For best results, store them in a plastic container and defrost in the fridge overnight before reheating.

Serving Suggestions

Ready to take these apple muffins with Greek yogurt on the go, serve at your next brunch buffet, or snack on one while relaxing on the couch? Here are a few ideas for pairing them!

• Enjoy them as a sweet finish to a savory breakfast, paired with scrambled eggs with Greek yogurt, or these make ahead mason jar scrambled eggs in the oven.
• Add them to your brunch buffet spread alongside this butternut squash breakfast, egg bake with sausage, and protein powder chia pudding.

Apple Yogurt Muffins Recipe FAQs