Easy Protein Mini Muffins with Greek Yogurt & Peanut Butter

If you love my Healthy Greek Yogurt Mini Muffins but want a version with a little more staying power, these protein mini muffins are it.

They’re still soft, still snack‑able, and still freezer‑friendly- just made with a few intentional swaps to bump up the protein without turning them into dense, dry “protein bakes.” These are the muffins I reach for when I want something quick that actually holds me over.

This recipe is based on my original Greek yogurt mini muffins, with a few changes to make them more protein‑focused. If you want the everyday, super flexible version, be sure to check out that post too.

What Makes These Protein Mini Muffins Different

Instead of completely reinventing the recipe, this version builds on the original with a few simple swaps:

• Peanut butter to replace one egg and add healthy fats
• A scoop of protein powder
• A little powdered peanut butter (PB2) for extra protein without weighing down the batter
• A little less flour to make up for the added powders

The result is a mini muffin that works well for snacks, lunchboxes, or a quick breakfast alongside fruit.

The Good Stuff Ingredient Swaps

While the full measurements are in the recipe card below, here is why I chose these specific “Good Stuff” ingredients for this recipe:

• Whole Cell Crushed Wheat: You can use all-purpose, but I love using whole cell crushed wheat or fresh milled flour for the extra nutrients. Check out my guide on the best flour swaps here!
• Whole Milk Greek Yogurt: This adds moisture and a serious protein boost. If you’re feeling ambitious, you can even use your own Homemade Yogurt.
• Honey or Maple Syrup: We skip the refined white sugar and use these instead. I’ve found that swapping sugar for natural sweeteners not only tastes better but avoids that mid-morning sugar crash.
• Real Vanilla Extract: Most store-bought vanillas are imitation “vanillin.” I always recommend using the real deal—you can see why in my Vanilla Simple Swap, or you can see how making your own vanilla is actually incredibly easy.
• Mini Chocolate Chips: I like using mini chips so you get a little chocolate in every bite without overdoing it, but regular chocolate chips will work also. For my favorite chocolate chips be sure to check out my chocolate chip swap!
• Peanut Butter: If you’re looking for a good peanut butter, you generally just need peanuts and salt in the ingredients, that’s it! If you want to know more about my go to peanut butter, check out my simple swap for peanut butter!

A Note About the Yogurt

I usually use my homemade crockpot Greek yogurt, which works great in this recipe. If you want to increase the protein a little more, you can use a high‑protein Greek yogurt from the store- some brands have a few extra grams per cup.

Either option works well, so use what you have.

A Note About the Flour

We use whole cell crushed wheat, but any all‑purpose flour or fresh milled flour will work. Since these are mini muffins and a quick bread, precision isn’t critical. If they come out slightly dry, reduce the flour just a bit next time. Some flours are higher in protein than others.

Instructions

1. Preheat your oven to 375°F and lightly grease a 24‑cup mini muffin pan
2. In a medium bowl, mix the flour, baking powder, baking soda, and salt.
3. In another bowl, whisk together the Greek yogurt, honey, melted butter, egg, peanut butter, protein powder, powdered peanut butter, and vanilla until smooth.
4. Pour the wet ingredients into the dry and gently fold until just combined. A few streaks of flour are fine- don’t over mix.
5. Stir in the chocolate chips.
6. Spoon batter into each muffin cup, filling them almost to the top.
7. Bake for 10–12 minutes, until lightly golden and a toothpick inserted in the center comes out clean.
8. Let the muffins cool in the pan for a few minutes, then transfer to a wire rack to finish cooling.

How Much Protein Is in Each Mini Muffin?

This batch makes 24 mini muffins-depending on the size of your mini muffin pan-they do vary.

Depending on the brands used, the full batch contains roughly 75–80 grams of protein total, which works out to about 3–3.5 grams of protein per mini muffin.

For comparison, most store‑bought mini muffins have less than 1 gram of protein each. These aren’t meant to replace a protein bar- just a more filling, higher‑protein muffin option.

Using a high‑protein Greek yogurt can bump that number slightly higher.

Storage & Freezing

• Store at room temperature for up to 2 days
• Refrigerate for up to 5 days
• Freeze for up to 3 months in an airtight container

They reheat well straight from the freezer.

Looking for the Original Version?

If you want a more flexible everyday muffin with lots of mix‑in options, check out my Healthy Greek Yogurt Mini Muffins. This protein version is based on that recipe with a few targeted swaps.

I’ve also converted the original recipe to include bananas in these Healthy Banana Chocolate Chip Mini Muffins with Greek Yogurt (No Refined Sugar)

This post contains affiliate links.

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Protein Mini Muffins with Greek Yogurt & Peanut Butter

Yield: 24 muffins

Prep Time: 5 minutes

: 10 minutes

Additional Time: 2 minutes

Total Time: 2 minutes

These protein mini muffins use Greek yogurt, peanut butter, and a scoop of protein powder for a soft, filling snack that’s easy to make ahead and freeze.

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Ingredients

• 3/4 cup flour
• 1 teaspoon baking powder
• 1/2 teaspoon baking soda
• 1/4 teaspoon salt
• 1 cup whole milk plain Greek yogurt
• 1/3 cup honey or maple syrup
• 1/4 cup unsalted butter, melted and slightly cooled
• 1 large egg
• 1/4 cup peanut butter
• 1 scoop vanilla protein powder
• 2 tablespoons powdered peanut butter (PB2)
• 2 teaspoons pure vanilla extract
• 1/2 cup mini chocolate chips

Instructions

1. Preheat your oven to 375°F and lightly grease a 24‑cup mini muffin pan.
2. In a medium bowl, mix the flour, baking powder, baking soda, and salt.
3. In another bowl, whisk together the Greek yogurt, honey, melted butter, egg, peanut butter, protein powder, powdered peanut butter, and vanilla until smooth.
4. Pour the wet ingredients into the dry and gently fold until just combined. A few streaks of flour are fine- don’t over mix.
5. Stir in the chocolate chips.
6. Spoon batter into each muffin cup, filling them almost to the top.
7. Bake for 10–12 minutes, until lightly golden and a toothpick inserted in the center comes out clean.
   Let the muffins cool in the pan for a few minutes, then transfer to a wire rack to finish cooling.

Notes

Find more recipes like this at thegoodstuffbakeshop.com

Nutrition Information:

Yield: 24 Serving Size: 2
Amount Per Serving:Calories: 235Total Fat: 11gSaturated Fat: 5gUnsaturated Fat: 6gCholesterol: 28mgSodium: 212mgCarbohydrates: 26gFiber: 2gSugar: 11gProtein: 9g

Nutrition information is calculated automatically as a courtesy and is an estimate only. Accuracy is not guaranteed as values can vary based on specific brands and preparation methods used.

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