15+ Healthy Muffin Recipes

Whether you enjoy them for breakfast, dessert or as an afternoon snack, these healthy muffin recipes are easy to make and delicious to eat.

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If you’re looking for some healthy muffin recipes to try, check out my top 18 muffins I’ve rounded out for you for inspiration. From chocolate muffins to peanut butter muffins and even sweet potato muffins, there’s something here for everyone! Grab them for breakfast, an afternoon pick-me-up, or a delicious dessert after dinner!

Round up of images for 10 muffin recipes
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Muffins don’t have to be loaded with sugar to enjoy! These 18 healthy muffin recipes are made with wholesome and natural ingredients that are nutritious for the whole family. These muffins are a great way to get some extra goodness into your diet. They are perfect for grab-and-go breakfasts, a great way to get a midday energy boost, and perfect to serve up as a delicious dessert.

Why You Should Bake More Healthy Muffin Recipes

  • Convenient hand-held servings and portion control. Muffins are already sized to individual servings, making them a convenient breakfast, snack, or dessert. You’ll also prevent overeating with the built-in portion control in muffins.
  • Great for meal prep. Muffins are incredibly freezer-friendly and can be a game-changer on busy mornings. Bake up a large batch on the weekend and pop them in the freezer for later enjoyment. Your future self will thank you.
  • Nutrient-packed deliciousness. These are truly some of the best healthy muffin recipes made with nutritious ingredients and using natural sweeteners and whole foods as much as possible.
  • Versatile flavors and textures. There’s a muffin out there for everyone. From muffins with fruit to rich chocolatey goodness and crunchy nuts, you’re sure to please everyone on your list with this roundup of healthy breakfast muffin recipes.

Tips for Making Healthy Muffin Recipes

  1. Don’t over mix your batter when making muffins. This can cause the gluten to over develop, and your muffins will be flat and chewy rather than light and fluffy. The dry ingredients should stirred in just until combined.
  2. Customize your muffins. It’s super easy to make your muffins exactly how you like them with simple add-ins. Chocolate chips, chopped nuts, dried and fresh fruits can be folded into the batter before you place them into muffin cups.
  3. Allow the muffins to cool before removing them from the pan. It’s tempting, but when you give it time, the steam that condenses around the muffins actually makes it easier to remove from the pan. And then don’t forget to cool them on the wire rack for about 15 minutes.
  4. Incorporate healthier ingredients. You’ll notice that many of these healthy breakfast muffin recipes contain ingredients like Greek yogurt and applesauce. These better-for-you ingredients add moisture and creaminess without the additional fat.
  5. Don’t let add-ins sink to the bottom. Berries, nuts, chocolate chips, and other add-ins tend to sink to the bottom. Give them a light dusting of flour to help them stay put in the batter.

Best Healthy Muffin Recipes

Muffins are a versatile food. They can be a delicious treat that also serves as a wholesome breakfast, part of your brunch spread, or a tasty afternoon snack to tie you over until dinner time. This roundup covers healthy breakfast muffin recipes to start the day on the right foot but also offers indulgent muffins with rich chocolate or seasonal fruit. Plus, you’ll love the low-sugar muffins that are sweetened with better-for-you sweeteners but satisfy your sweet cravings.

Healthy Breakfast Muffins

  • Bran Muffins with Dates – These bran muffins strike the perfect balance between healthy and delicious! With wheat bran, whole wheat flour, and sweetened with maple syrup, they’re loaded with fiber for a filling breakfast.
  • Apple Cinnamon Oatmeal Cups – This is a cross between baked oatmeal and muffins and makes for the most perfectly healthy breakfast. Think oatmeal in individual-sized, hand-held servings – just what you need on busy mornings!
  • Gluten-Free Banana Chocolate Chip Muffins – Quick, easy, satisfying, and oh-so-delicious. This is a must-try on your list of healthy breakfast muffin recipes. It’s made with Greek yogurt, rolled oats, bananas, and subtly sweetened with honey, making this breakfast taste like a real treat.
  • Healthy Banana Nut Muffins – Made with wholesome ingredients like whole wheat flour and rolled oats, these healthy breakfast muffins are a satisfying start to your day. Better yet, take the morning stress away, meal-prep them on the weekend, and be set all week long.
  • Kid-Friendly Muffins – If you’re looking for healthy breakfast muffin recipes that kids of all ages will love – this one checks all the boxes. You’ll find a sweet version made with peanut butter and strawberry jam and a savory muffin made with grated zucchini and shredded cheddar cheese.

Low Sugar Muffins

  • Sweet Potato Muffins – Oil free, low in sugar, and filled with nutrition, this is one of the best healthy breakfast muffins out there. They’re naturally vegan and easy to whip up with everyday ingredients but provide that satisfying taste that we all love.
  • Carrot Cake Muffins – Sweetened with honey and packed with nutrition from Greek yogurt, carrots, raisins, and walnuts, these low sugar muffins are a treat that seamlessly blends wholesome ingredients with delightful flavor.
  • Peanut Butter Banana Muffins – With less than 9 grams of sugar per serving, these muffins are perfect for an easy on-the-go breakfast or snack without sacrificing the deliciousness you crave in the mornings.
  • Pizza Muffins – These savory muffins are a playful spin on traditional pizza, with all the goodness of pizza flavors and textures tucked neatly into muffin-sized packages. Compact, hand-held ooey-gooey pizza bites that kids and adults alike will absolutely adore!

Healthy Muffin Recipes with Fruit

  • Apple Cinnamon Muffins – You’ll love this one-bowl muffin recipe. They have that classic apple-cinnamon combo everyone loves with chunks of apples in every bite. The addition of Greek yogurt and coconut sugar makes this one of the best healthy breakfast muffins!
  • Blueberry Banana Muffins – Subtly sweetened with bananas and a little bit of brown sugar, these low sugar muffins are a great way to start the day or enjoy as a mid-afternoon snack with a cup of tea.
  • Cranberry Lemon Muffins – Perfect for last-minute holiday guests or just as a treat for your family any time of the year using frozen cranberries. These muffins have a zesty, tangy flavor and perfectly moist texture that will leave your taste buds happy.
  • Pumpkin Banana Muffins – These muffins require minimal effort for maximum deliciousness. Be sure to add this 20-minute recipe to your repertoire of healthy breakfast muffins but they’re also great as an afternoon pick-me-up or a treat after dinner.

Sweet Muffins

  • Zucchini Bread Muffins – Nothing screams healthy breakfast muffin recipes more than sneaking in some veggies. This zucchini bread turned into a muffin recipe proves that nutritious can be delicious and it’s loved by adults and kids alike!
  • Chocolate Banana Muffins – Easy to whip up in one bowl, this will become one of your favorite healthy muffin recipes because it’s made with Greek yogurt, coconut oil, and sweetened with bananas and a touch of honey.
  • Chai Spiced Vegan Muffins – A healthy breakfast or snack filled with warm aromatic spices like cloves, cinnamon, ginger, and cardamom. It’s sweetened with coconut sugar and a touch of natural applesauce and has only 11 grams of sugar, making it one of the tastiest low sugar muffins.
  • Double Chocolate Muffins – This is a real treat for all chocolate lovers. It’s loaded with cocoa and chocolate chips, promising double the chocolate flavor. Plus, it calls for better-for-you ingredients like applesauce and oat flour, so you’ll actually feel good about enjoying this treat that feels so indulgent.
  • Banana Bread Muffins – Whip up a batch of banana bread muffins in under 30 minutes that’s perfect for breakfast, brunch, or a quick snack. They have a perfectly soft and moist interior with crunchy walnuts in every bite.

How To Store Muffins

  • Store at room temperature. Freshly baked muffins can be stored in an airtight container for 1 to 2 days at room temperature if they don’t contain perishable ingredients like dairy or fresh fruit.
  • Store in the refrigerator. After that, transfer them to the fridge for up to 4-5 days. Place a piece of paper towel in the bottom of your container to absorb any moisture and ensure the container is sealed tightly.
  • To freeze muffins. For longer storage, muffins can be frozen. Wrap each muffin individually in plastic wrap and place them in a sealed container or zip-top bag to prevent freezer burn. Freeze for up to 3 months. Thaw at room temperature for a few hours before enjoying.
  • To reheat muffins. Some muffins taste best when warm, especially if they have been previously frozen. To refresh the texture of the muffins, you can briefly warm them in a small toaster oven at low temperature for 5 minutes or until warmed through.
  • Avoid moisture. To prevent the muffins from becoming soggy, avoid storing them in a container that traps moisture, and if you see condensation forming inside the container, transfer them to a different container. Be sure you add a piece of paper towel to absorb any moisture.

Frequently Asked Questions

What makes a muffin healthy or unhealthy?

The term healthy is highly subjective, but it generally means that they are made with wholesome and nutritious ingredients, including whole grains, fruits, nuts, and do not contain excessive amounts of sugar or unhealthy fats.

How can I prevent the muffins from sticking to the muffin pan?

Getting your muffins stuck to the muffin tin can be annoying but you can avoid that by using non-stick muffin tin or line the cups with paper or silicone liners. Alternatively, you can also lightly grease the cups with cooking spray or a small amount of oil.

Can I make these muffins gluten-free?

Most healthy breakfast muffins can be made with a gluten-free flour blend that has a 1:1 substitution ratio. However, I have not personally tested them all, and it’s best to follow the recipe as written. It’s also important to note that you cannot swap the regular wheat flour with almond or coconut flour as the properties differ.

Whole wheat bran muffins in a clothed lined pan for serving.

These healthy breakfast muffin recipes are a delicious way to start the day. But don’t limit them to breakfast only. They’re easy to whip up on a lazy afternoon as a great pick-me-up snack or tasty dessert in the evening. Either way, this roundup has you covered from morning to night with a variety of wholesome and flavorful options.

Full List of Recipes

Check out the picture cards for all the recipes listed above. You can click on any of the recipes cards to take you directly to those recipes.

Bran muffins in a cloth lined pan.

Bran Muffins

Fuel your morning with a wholesome bran muffin, packed with the goodness of dates and added sweetness of maple syrup.
32 minutes
5 from 33 votes
Large plate of apple cinnamon oatmeal cups

Apple Cinnamon Oatmeal Cups

This Apple Cinnamon Oatmeal Cups recipe is a cross between baked oatmeal & muffins. It's made with simple vegan ingredients & makes for a healthy breakfast!
40 minutes
4.9 from 46 votes
Overhead view of chocolate chip muffins on a large plate with one off to the side.
Breakfast, Dessert

Banana Chocolate Chip Muffins

Gluten-Free Banana Chocolate Chip Muffins that are made completely with no oil and no refined sugar but they’re bursting with wholesome goodness and flavor!
30 minutes
5 from 24 votes
Healthy banana nut muffins on. a wire wrack

Healthy Banana Nut Muffins

Healthy Banana Nut Muffins are made with wholesome ingredients like whole wheat flour and whole grain oats with no butter or refined sugar – moist & fluffy!
40 minutes
5 from 35 votes
Healthy muffins on a plate.
Breakfast, Dessert

Healthy Muffins for Kids

These healthy muffins for kids are great for grab-and-go breakfast, lunchbox or snacks. They're filled with wholesome ingredients for a nutritious tasty treat.
35 minutes
5 from 772 votes
Soft and moist sweet potato muffins stacked on a plate with the paper liner pulled away from a few.
Breakfast, Snack

Sweet Potato Muffins

Try these vegan Sweet Potato Muffins made with easy ingredients in 30 minutes. They are kid-friendly and nutritious – great for breakfast or school lunchbox
35 minutes
4.9 from 251 votes
Carrot cake muffins on a wooden board
Breakfast, Dessert, Snack

Carrot Cake Muffins

Quick and easy to make, these carrot cake muffins are the perfect treat for Easter. Made with natural and healthy ingredients, they are perfectly moist.
35 minutes
4.9 from 45 votes
Peanut butter banana muffins in a pan topped with slices of bananas
Breakfast, Snack

Peanut Butter Banana Muffins

Easy and quick to make, these healthy peanut butter banana muffins are perfect for the whole family. Gluten-free and dairy-free with no artificial sugar.
25 minutes
5 from 87 votes
Pizza muffins in muffin pan.
Appetizer, Lunch, Snack

Pizza Muffins

These pizza muffins are stuffed with cheesy goodness! They are perfect bites of pizza to eat as a snack, appetizer or even dinner.
35 minutes
5 from 7 votes
Plate of apple cinnamon muffins with one cut in half to show the apple pieces

Apple Cinnamon Muffins

These Apple Cinnamon Muffins are a simple one-bowl breakfast recipe made with no oil and loaded with fresh apples – perfect treat for fall!
45 minutes
5 from 54 votes
Banana blueberry muffins after baking and cooling on a wire rack.

Banana Blueberry Muffins

These Banana Blueberry Muffins are made with Greek yogurt, fresh blueberries, and bananas for a moist breakfast-time treat! Perfect for meal-prep!
30 minutes
4.9 from 533 votes
Muffin tin with baked cranberry muffins, and cranberries added in two of the muffin tins

Cranberry Lemon Muffins

This easy recipe for Cranberry Lemon Muffins is perfect for last minute holiday guests. They have a zesty tangy flavor and a moist texture.
37 minutes
5 from 123 votes
Pumpkin banana muffins on a plate.
Breakfast, Dessert

Pumpkin Banana Muffins

These Pumpkin Banana Muffins are moist and perfectly balanced with warm spices and ripe banana sweetness, making them perfect for fall.
30 minutes
5 from 180 votes
Zucchini bread muffins in a large platter with
Breakfast, Snack

Zucchini Bread Muffins

These simple to make healthy zucchini bread muffins are a delicious treat the whole family will love. Perfectly fluffy and quick to make in one bowl.
35 minutes
5 from 40 votes
Chocolate banana muffins on a white plate with a bite taken out of one of them
Breakfast, Dessert, Snack

Chocolate Banana Muffins

These Chocolate Banana Muffins are easy to whip up in one bowl and made healthy with Greek yogurt and coconut oil – perfect snack or treat!
35 minutes
5 from 61 votes
Large basket of the chia spiced muffins

Chai Spiced Vegan Muffins

This Chai Spiced Vegan Muffins recipe is a delicious healthy breakfast or snack filled with warm aromatic spices like cloves, cinnamon, ginger and cardamom!
30 minutes
5 from 40 votes
Bite taken out of double chocolate chip muffin

Double Chocolate Chip Muffins

This Double Chocolate Chip Muffins recipe is only 150 calories per muffin. It's loaded with cocoa and chocolate chips – a real treat for chocolate lovers!
38 minutes
5 from 16 votes
8 banana bread muffins stacked on a plate with a small dish of walnuts and a few extra muffins off plate.

Banana Bread Muffins

Bake up a batch of Banana Bread Muffins with crunchy walnuts. Perfect for breakfast, brunch, or a quick snack in under 30 minutes.
30 minutes
5 from 49 votes

For more similar roundup of recipes, be sure to check out: Easy and Healthy Recipes with Oats, Freezer Meals, Everyday Breakfast Ideas, and Recipes to Make with Pantry Staples.

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