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Apple Pie Protein Muffins

5 from 38 votes

Soft, moist, and packed with nutrition, these healthy apple pie protein muffins are a wonderful family friendly healthy snack!

Apple Protein Muffins

Healthy apple pie protein muffin recipe

I’ve already made these apple muffins three times in the past month.

With sweet apples and cinnamon swirled into every delicious bite, they are truly something special.

For breakfast, snack, or packed into a school lunch box, there’s never a wrong time to enjoy the charms of these wholesome and high protein apple pie muffins.

You may also like these Healthy Blueberry Muffins

Apple Pie Muffin Ingredients With Protein Powder

Ingredients for apple protein muffins

The easy muffin recipe calls for applesauce, protein powder, flour, cinnamon, sugar, baking soda, salt, baking powder, white or apple cider vinegar, pure vanilla extract, water, optional oil or nut butter, and finely diced apple.

Either sweetened or unsweetened applesauce are fine to use. If you do not have applesauce on hand, you may substitute an equal amount of mashed banana. Or substitute Greek yogurt or canned pumpkin, increasing the sweetener to half a cup to make up for the difference in sweetness.

I used unsweetened and unflavored pea protein powder. You may also try something like cinnamon roll, vanilla, pumpkin pie, or caramel protein powder. Be sure to use a brand and flavor of protein that you already know you like.

If desired, you may substitute unrefined coconut sugar, date sugar, brown sugar, or sugar free xylitol for the sugar.

Spelt flour, white flour, and some brands of all purpose gluten free flour work. Or you can use oat flour to make apple oatmeal muffins.

I have not tried coconut flour, almond flour, or whole wheat flour here and therefore cannot recommend any of those in this recipe.

Depending on the specific ingredients you use, the fluffy apple muffins can be egg free, dairy free, vegan, gluten free, low fat, low calorie, and oil free.

The recipe was adapted from these Protein Muffins

High Protein Snack Muffins Recipe

How to make the apple cinnamon muffin recipe

Preheat the oven to 350 degrees Fahrenheit.

Line a muffin tin with cupcake liners, or grease the pan with oil spray.

In a large bowl, whisk together the water, applesauce, pure vanilla extract, vinegar, diced apples, and optional oil or nut butter.

Add the flour, protein powder, dry sweetener, cinnamon, salt, baking soda, and baking powder to the bowl with the liquid ingredients. Stir until just evenly combined.

(If you prefer, feel free to mix the dry ingredients weeks in advance. Store this dry mix in an airtight container or bag until ready to use.)

Scoop the apple muffin batter into the prepared muffin tray, dividing the batter evenly among each greased or lined muffin cup.

Bake on the oven’s center rack for nineteen minutes. The muffins are done when a toothpick inserted into the center of a muffin comes out mostly clean.

Allow the pan to cool for around ten minutes before removing the muffins.

Once cooled, if you let them sit on the counter or in the refrigerator, loosely covered with cloth or paper towels, the liners should peel off easily by the next day.

Girl Apple Picking Basket

Recipe variations

I often like to replace half a cup of the diced apples with fresh blueberries.

You could do the same with diced strawberries or cherries.

The muffins are also wonderful with half a cup of raisins or a handful of shredded coconut or dried cranberries or dates stirred into the mix.

Apple Muffin Recipe Video

Watch the step-by-step apple protein muffin video above

High Protein Apple Muffin Recipe
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Apple Pie Protein Muffins

These healthy apple pie protein muffins are a wonderful family friendly healthy snack recipe.
Cook Time 19 minutes
Total Time 19 minutes
Yield 12 muffins
5 from 38 votes


  • 1/2 cup applesauce
  • 1/2 cup water
  • 3 tbsp oil, nut butter, or additional water
  • 1 tsp pure vanilla extract
  • 2 1/2 tsp white or cider vinegar
  • 2/3 cup flour (Or try these low carb Keto Muffins)
  • 1/2 cup protein powder
  • 1/3 cup sugar, unrefined if desired
  • 2 tsp cinnamon
  • 1/2 tsp each: baking powder, baking soda, and salt
  • 1 1/2 cups finely diced apple (150g)


  • Preheat oven to 350 F. Grease or line a muffin tin. Whisk wet ingredients, including apple. Stir in remaining ingredients just until evenly mixed. Divide among the muffin tins. Bake 19 minutes for large muffins or 12 minutes for mini muffins. The muffins are done baking when a toothpick inserted into the center comes out mostly clean. Let cool before removing from the tins. If you use liners and let them sit loosely covered overnight, the liners should peel off easily after a day.
    View Nutrition Facts


Use leftover protein powder to make Protein Banana Bread.

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Published on October 4, 2023

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  1. Michi says

    Something is missing, or the amount of flour in the recipe is wrong. How much flour (or other ingredients should really be in there?

    • CCK Media Team says

      The amounts are correct, and we have made this recipe at least twenty times, so it definitely works as written. The batter will look like it does in the video. Try it and see! 🙂

      • Sarah says

        My batter was very watery/runnny and I made exactly like the recipe says.

        I do see in the video it looks like she does only 1 tbs of oil or water and the recipe says 3 tbs?

        The batter looks nothing like the video.

        • Chocolate Covered Katie says

          Are you looking at the vinegar by chance? The water in the video is added from the silver measuring cup. It is definitely more than a tablespoon. Perhaps your protein powder is making your batter thinner. I highly recommend pea protein powder – it works perfectly here!

  2. Allyson Widlak says

    5 stars
    These muffins are fantastic! I had no applesauce so I used bananas, did only water and actually substituted oat flour(I wouldn’t necessarily recommend that) they still came out amazing! A little grainy and I thought I’d be the only one eating them but all my kids and my picky husband loved them! Thanks!

5 from 38 votes (37 ratings without comment)

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