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23 Healthy Muffin Recipes

The best Healthy Muffin Recipes, perfect for when you need an easy breakfast idea or snack. From blueberry muffins to banana muffins and more, this recipe collection includes a muffin for every craving.

Healthy banana muffins on parchment paper with cinnamon sprinkled around.

When I want to bake something quick, sweet and on the healthy side, muffins are my go-to. I’ve shared so many easy muffin recipes over the years, and I wanted to collect them together in one place to make them easy to find. 

Below you’ll find a healthier twist on many classic muffin recipes. These recipes use wholesome ingredients such as whole wheat flour, applesauce and mashed banana to create crave-worthy muffins for every occasion, from a weekend brunch to after school snacks.

These muffins bake up slightly sweet and fluffy, and include a variety of mix-ins. Fresh berries, vegetables (zucchini and carrots!), chocolate chips, peanut butter… you’ll love all of the delicious options in this collection of muffin recipes. All of these muffins freeze well for a quick make ahead breakfast or snack, and you’ll find my tips for storing muffins below. Now let’s get baking!

Blueberry Muffin Recipes

Always a favorite, blueberry muffins deliver sweet bites of juicy berries in a soft and tender muffin. Frozen blueberries work just as well as fresh in these recipes, so you can enjoy them year-round.

healthy blueberry muffins with fresh blueberries

Blueberry Muffins

This quick and easy blueberry muffin recipe comes together in one bowl in just a few minutes. Naturally sweetened with honey or pure maple syrup, this light and fluffy blueberry muffin recipe is my healthy take on the classic.

Blueberry oatmeal muffins stacked on muffin pan.

Blueberry Oatmeal Muffins

Try not to eat them all! Perfect for snacking, these wholesome blueberry muffins are filled with good-for-you ingredients, including whole wheat flour, old fashioned rolled oats and blueberries. 

blueberry banana muffin with muffins in backround.

Blueberry Banana Muffins

Everyone loves the muffin combination of blueberries and banana! Sweetened with bananas and maple syrup this is a refined sugar free muffin recipe that is so delicious you’ll make them again and again. (Also try this Blueberry Banana Bread.) 

Banana Muffin Recipes

If you ask me, you can never have too many varieties of banana muffins! From a basic banana muffin to homemade muffins made with peanut butter, chocolate and apple, adults and kids alike are sure to gobble these up.

Healthy Banana Muffins

With a batter that takes just minutes to mix up, these healthy banana muffins are an all-time favorite. Lightly spiced with cinnamon, these muffins have all the banana flavor you love. 

These flourless Healthy Blender Banana Muffins are dairy-free and gluten-free. They are quick and easy to make in your blender! These healthy muffins freeze well for meal prep breakfasts and snacks!

Blender Banana Muffins

Have you tried making muffins in your blender? It is the EASIEST way to make them! These dairy-free and flourless banana muffins take 10 minutes to prep for the oven. Since everything is mixed together in your blender, clean up is quick and easy, too.

Close up of peanut butter banana muffin with chocolate chips with muffin pan in background.

Peanut Butter Banana Muffins

Fans of the classic peanut butter and banana combination will love these! Six grams of protein and a satisfying peanut butter and banana flavor make these muffins a wholesome, filling snack. Plus, who can resist chocolate chip muffins? 

Close up of almond butter banana muffins with chocolate chips.

Almond Butter Banana Muffins

These muffins are part sweet treat, part healthy protein and fats from almond butter, flaxseeds and whole grains. This banana muffin is the perfect satisfying snack. 

banana granola muffin on a wire rack.

Banana Granola Muffins

Sweet banana muffins with toasted nuts and a crunchy granola topping are a fun twist on the classic banana muffin. Use store-bought or homemade granola to make these delicious muffins.

Close up of a chocolate banana muffin with chocolate chips.

Chocolate Banana Muffins

These double chocolate muffins are sweetened with banana and honey and studded with chocolate chips. Warm from the oven they’re simply irresistible! 

Close up of apple banana muffin with cluster of muffins in background and banana to the side.

Apple Banana Muffins

Apple and banana are a delicious combination in these fluffy muffins! Made with honey, whole wheat flour and cinnamon, this easy muffin recipe is a crowd pleaser.

Egg Muffin Recipes

Shake up your breakfast routine with one of these easy egg muffin recipes! These savory muffins are a great way to sneak some veggies and satiating protein into your morning meal.

Stack of 3 egg muffins with veggies and feta.Egg Muffins

These egg muffins are full of flavor and packed with protein and good-for-you veggies. Make them ahead for any easy grab and go breakfast

Ham, Cheese, and Veggie Frittata muffins on a plate.

Frittata Muffins

Enjoy a complete ham, egg and cheese omelet in a muffin cup with these easy mini frittatas made in a muffin pan. 

3 mini frittata muffins on a plate with peaches and toast.

Mini Frittata Muffins

Broccoli Cheddar Mini Frittatas are delicious and healthy little bites! Made in a mini muffin pan, these frittata muffins are the perfect breakfast for busy mornings that you can make-ahead and freeze.

Cozy Fall Muffin Recipes

From pumpkin and spice to apples and cranberries, these cozy muffin recipes are a delightful way to welcome the autumn season.

The BEST Pumpkin Chocolate Chip Muffins are so easy to make in one bowl! These healthy muffins are soft and filled with pumpkin pie spice! Dairy free and vegan options.

Pumpkin Muffins

These are the perfectly spiced fall muffin with pumpkin. Made with whole grains and sweetened with honey, one batch won’t last long! (Neither will the best pumpkin bread.) 

Pumpkin coffee cake muffin with more muffins in background.

Pumpkin Coffee Cake Muffins

A fall treat, these pumpkin coffee cake muffins have a delicious crumble topping. They’re filled with warm spices and perfect for enjoying with a cup of coffee or tea. 

Applesauce muffins stacked close together.

Applesauce Muffins

Fresh apples, applesauce and cinnamon star in this cozy fall muffin. They’re freezer-friendly and a perfect healthy snack for the kids. 

Two spice muffins with mini chocolate chips stacked on top of each other.

Spice Muffins

Grab a cup of tea and take a moment to unwind with one of these healthy spice muffins. Filled with warm spices including cinnamon, cardamom and cloves, a touch of orange, and (optional) chocolate chips, these are irresistible.

cranberry orange muffins stacked together

Cranberry Orange Muffins

These fresh cranberry muffins are healthy and full of sweet-tart cranberry orange flavor. These muffins are perfect for a holiday brunch, Christmas morning or an afternoon treat. 

More Favorite Muffin Recipes

More muffins to love! Zucchini muffins, fresh strawberry muffins, healthy muffins that taste like brownies… these easy muffin recipes can’t be missed! 

Chocolate Black Bean Blender Muffins, three muffins stacked on top of each other.

Chocolate Black Bean Blender Muffins

These high protein blender muffins are disguised as a delicious chocolate muffin that even my kids love. They’re just like a black bean brownie, but in muffin form.

Close up of a zucchini muffin with a pile of muffins in the background and a fresh zucchini on the side.

Zucchini Muffins

Moist, flavorful and healthy, these muffins made with zucchini are great way to start your day. Or, enjoy them as a healthy snack. 

Strawberry muffins on a wire rack.

Strawberry Muffins

These strawberry muffins are so addictive, it’s a good thing they’re made with healthier ingredients! With these muffins you get a tender whole wheat muffin base that’s naturally sweetened with honey or pure maple syrup. Plus there are sweet fresh strawberries in every bite!

health carrot cake muffins on a plate

Healthy Carrot Cake Muffins

These carrot cake muffins are ridiculously tasty, and good for you too! This muffin recipe is sweetened with pure maple syrup and packs plenty of whole grains to leave you feeling satisfied. 

Grapefruit ricotta muffins with icing on a cooling rack.

Grapefruit Ricotta Muffins

You will love the moist texture that ricotta cheese brings to muffins! This unique muffin flavor has a subtle tanginess from grapefruit zest and juice, which pairs perfectly with the sweet glaze.

Muffin Recipe Tips

  • When adding baking powder, baking soda and salt mix well with a whisk. You don’t want any clumps of these ingredients left in the muffin batter.
  • When measuring the flour, lightly spoon it into your measuring cup and then level it off. Scooping the flour directly with the measuring cup can cause too much flour to get packed in.
  • After adding the flour mix until just combined. Over mixing can lead to dense muffins.
  • A large trigger-style ice cream scoop makes portioning your muffins quick and easy.
  • This is my absolute favorite muffin pan. It is completely nonstick! I never spray it with cooking spray or use paper liners and my muffins never stick to the pan.

How to Store Muffins

Muffins can be stored at room temperature or in the freezer. To store at room temperature, line the bottom of an airtight container with a paper towel and place the muffins on the paper towel. Most muffins will stay fresh this way for up to 2-3 days. Muffins that have a lot of moisture, such as strawberry muffins or black bean muffins, are best stored in the freezer.

How to Freeze Muffins

I always store any leftover muffins in the freezer because they stay freshest that way. Let the muffins cool completely on a wire rack and then store them in an airtight container in the freezer for up to 3 months. I like to store them in a zip-top plastic bag because it allows you to squeeze out any extra air that could lead to freezer burn. 

To thaw a frozen muffin:

  • Let it sit at room temperature for 20-30 minutes. 
  • Or, use your microwave’s defrost setting to gently thaw and warm.
  • Or, place muffins in the refrigerator overnight to thaw.

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