Cherry Muffin Recipe {Healthy and High Protein}

Imagine bakery-style muffins packed with protein, soft and nutty, and bursting with juicy cherries—this Cherry Muffin Recipe is just that! It’s perfect for breakfast, a quick snack, or whenever you want something sweet yet nourishing.

9 grams of Protein in every single muffin!

Cherry and pistachio are popping up everywhere lately—think lattes, scones, and all kinds of fun combinations. I took inspiration from my popular Protein Blueberry Muffins and whipped up these bakery-worthy cherry muffins with a protein punch of 9 grams each—perfect for cherry season!

Think about that: juicy fresh cherries nestled in a tender, fluffy muffin. These homemade cherry muffins hit the perfect sweet and tart note, while giving you a satisfying boost with simple ingredients and added protein. They taste like you just bought them at your favorite cozy bakery.

If you’re a muffin fan looking for other crowd-pleasers with top ratings, you should check out my Greek Yogurt Banana Muffins, Oatmeal Raisin Muffins, or these incredibly easy One Bowl Double Chocolate Chip Muffins. They’re family favorites you’re going to love as much as these cherry ones!

Recipe Ingredients

• Flour – I used all-purpose flour here. I haven’t tested with alternatives, so swap carefully if you want to experiment.
• Sweetener – This recipe strikes a great balance with brown sugar and maple syrup for a rich, natural sweetness.
• Greek Yogurt – It makes the muffins super moist and adds richness without heaviness.
• Milk – I went with whole milk, but you can easily swap in your favorite dairy-free milk.
• Almond Extract – Just a little almond extract brings out that classic amaretto vibe that pairs perfectly with tart cherries, like the magical flavor in cherry garcia ice cream.
• Vanilla Protein Powder – I used CleanSimple Eats brand Protein Powder, but any vanilla one works okay.
• Baking Agents – The usual suspects: baking powder, baking soda, eggs, and salt to help everything rise and taste just right.
• Oil – I recommend vegetable or avocado oil. Melted butter will work great if you prefer.
• Cherries – Fresh, sweet cherries are the star here. I pitted and sliced mine, but thawed frozen cherries are fine too. For a sweeter muffin, maraschino cherries work as a fun twist.
• Pistachios – For texture and flavor, chopped pistachios are fantastic. You can swap almonds if that’s what you have on hand.

Check the recipe card below for the complete ingredient list and exact measurements.

Substitutions and Variations

• Change up your mix-ins! Feel free to fold in chopped nuts for crunch, dark or white chocolate chips, or swap in seasonal berries for a fresh twist.
• No protein powder? No problem. Just add an extra ¼ cup of flour to make up the difference since protein powder absorbs liquid differently than flour.
• Want a bakery-style finish? Try a streusel topping made from ¼ cup crushed pistachios, 2 tablespoons flour, 2 tablespoons brown sugar, and 1 tablespoon softened butter. Mix it all up and sprinkle generously on top before baking.
• For a richer muffin, swap the Greek yogurt with sour cream. Yogurt keeps it lighter and adds protein, while sour cream makes the crumb more tender and indulgent. It’s your call depending on how you want to enjoy them!

How to Make This Recipe

1. Start by preheating your oven to 425°F. Line your muffin tin with liners and spray them lightly with cooking spray.

2. In a medium bowl, combine all the wet ingredients. Use a handheld electric mixer to beat until the mixture is smooth and uniform.

3. In another bowl, mix together all the dry ingredients. I know, extra dishes, right? But when you bake with protein powder, it’s super important to mix the dry ingredients well to keep everything evenly distributed.

4. Slowly pour the dry mix into the bowl with the wet ingredients. Use a whisk to gently fold them together until smooth. Be sure to scrape the sides of the bowl as you go. Next, fold in the oil until the batter is silky and smooth. Finally, gently fold in the chopped cherries and crushed pistachios.

5. Grab a 3-tablespoon cookie scoop to distribute the batter evenly into the muffin liners—you want the batter to fill each liner to the top, but not overflow. Once filled, sprinkle a few extra cherry chunks, some crushed pistachios, and a teaspoon of turbinado sugar over each muffin for that beautiful bakery finish.

6. Pop the muffins in the oven and bake at 425°F for 5 minutes. Without opening the oven, lower the heat to 350°F and continue baking for 15 to 18 more minutes. You’ll know they’re done when the tops turn golden and a toothpick inserted in the middle comes out clean or with a few moist crumbs attached. Enjoy them warm or at room temperature! Pro tip: follow the 200°F rule! When the inside of the muffin reaches 200°F, it’s perfectly cooked.

PRO TIPS

• Uniform muffins bake better and look prettier! Using a cookie scoop helps portion the batter evenly, which means no mystery muffin sizing and less mess too.
• Whisk your dry ingredients gently but well to keep the batter from overmixing. Overmixing can make your muffins flat and tough instead of fluffy and tender.

Recipe FAQs

How should I store these muffins?

Keep muffins in an airtight container at room temperature for up to three days. If you want to make them last longer, wrap them individually and freeze in a zipped bag—this way, you have easy, grab-and-go breakfast options. To reheat, wrap in foil and warm in a toaster oven for that fresh-out-of-the-oven feel.

Do I have to use muffin liners?

I recommend using muffin liners for this recipe, especially because the protein powder and yogurt make these muffins moist and sticky. Liners make cleanup a breeze, help the muffins keep their shape, and are great for freezing or storing. If you don’t have liners, just grease your muffin pan really well—using both butter and cooking spray is a great way to avoid sticking.

Why did my muffins turn out dry or crumbly?

This usually happens if the batter is overmixed or the muffins bake too long. For tender, moist muffins, mix just until the ingredients come together and check for doneness a couple minutes before the timer goes off.

Serving suggestions

Cherry muffins call for something creamy, fresh, or lightly savory alongside to balance those flavors. Try them with a dollop of Greek yogurt, some whipped ricotta, or a handful of fresh berries for a fresh boost.

If you’d like something savory, soft goat cheese scrambled eggs or a mild cheese pairs wonderfully. To wash it all down, grab a cold brew coffee, a warm chai tea, or for a fun flavor echo, try a cherry chocolate smoothie.