These 21 Healthy Muffin Recipes are perfect for enjoying as a wholesome breakfast, snack, or dessert. This list includes delicious healthy muffins for kids and adults.

Best healthy muffin recipes photos of muffins.

Below is a list of healthy muffin recipes that are packed with flavor and wholesome ingredients. So whether you’re looking for healthy breakfast muffins, healthy muffins for kids, or even gluten-free muffin recipes, this list contains something for everyone!

Best of all, most of homemade muffins below are meal prep and freezer friendly. I recommend making a double batch, ready to enjoy chilled or reheated for breakfast, snack or dessert.

Let me know in the comments which of these healthy muffin recipes is your favorite!

Tips for Baking Healthy Muffin Recipes

Here are my top tips for making healthy muffins I have learnt over the years in the kitchen.

  • Always follow the recipe: Baking is a science! Unlike with soups when it comes to baking, 99% of times you have to follow the recipe. Main reason is not to offset the ratio of dry to liquid ingredients.
  • Do not substitute flours: All flours act differently in baking! Coconut flour is more absorbing that wheat flour. Oat flour weighs less than wheat flour. And almond flour is made out of nuts and doesn’t absorb moisture at all. Unless healthy muffin recipe lists an acceptable swap, I recommend to follow the recipe as close as possible!
  • Don’t overmix the batter: When making muffins with gluten, make sure not to overmix the batter if you don’t want dense and chewy results. Instead, the wet ingredients and dry ingredients should be mixed until just combined. Don’t worry if there are some lumps or white patches of flour, it’s normal.
  • Use the spoon and level method: When measuring flour so you don’t end up with dense muffins. The best way to do this is to spoon the ingredient into the cup and then use the back of a knife to level the top. Watch this quick tutorial how to do it properly.
  • Don’t over bake your healthy muffins: Bake as long as recipe says or until a toothpick inserted in the center comes out clean. Even if your healthy muffins do not look brown enough, remove them from the oven after a toothpick test. They will keep cooking with residual heat.
  • Check the leavening agents: This tip goes for any baking with leavening agents. To test baking powder, combine 1 teaspoon with 1/4 cup hot water and watch for immediate fizzing. To test baking soda, use a small splash of vinegar instead of water.
  • Storage: Check out my posts how to store muffins and how to freeze muffins for all my best storage tips and tricks.

More FAQs

What makes muffins healthy?

For healthy muffin recipes, I try to minimize empty calories by relying on more nutritious flours, unrefined sweeteners, using less oil or yogurt and applesauce instead of it. The result are muffins packed with fiber, whole grains, natural sweeteners, and healthy fats. They won’t spike your blood sugars or have you craving more snacks.

What does applesauce do to muffins?

Applesauce replaces oil and makes muffins moist cutting back on calories and fat. In most healthy muffin recipes, I still recommend to add even a few tablespoons of oil to make muffins less gummy.

When can I use yogurt instead of applesauce?

You can substitute applesauce for yogurt in most muffin recipes. Keep in mind yogurt is tangy and less sweet than applesauce, so be sure to add 2-3 tablespoons of maple syrup or sugar to compensate for it. It should not offset your muffin batter consistency.

Can I use all-purpose flour instead of whole wheat flour?

Yes and no. Some muffin recipes can take this 1:1 substitution but most cannot. General rule of thumb is to use 1 cup of white flour for every 3/4 cup of whole wheat flour that the recipe calls for.

What whole grain flours can I substitute at 1:1 ratio?

When it comes to healthy muffin recipes with whole wheat flour, you can use spelt flour, white whole wheat flour or whole wheat pastry flour at 1:1 ratio. With almond flour recipes, most recipes can be made with 1:1 almond meal for almond flour but muffins will be more dense and rise less.

How can I use gluten-free flours in your healthy muffin recipes?

I find all gluten-free flours need adjustments. It’s best to follow the recipe as is or check the recipe post for any substitutions tips first. You can’t substitute coconut flour with any other flour. You may use all-purpose gluten free flour instead of wheat flour but will need to add a splash of milk. Substitute oat flour by weight – 1 cup of oat flour weighs 90 grams and 1 cup of wheat flour weighs 120 grams.

How can I make healthy muffins without eggs?

Most of my healthy muffin recipes can be made egg free by using a flax egg or chia seed egg, except muffins with almond flour where eggs act as major binder. Expect more dense and less fluffy muffins with vegan “eggs”.

What makes healthy muffins light and fluffy?

Leavening agents like baking powder and baking soda help provide lift and texture to the muffins. More so, with a little healthy fat or oil, muffins are made lighter too. One of the best tips for making light and fluffy whole grain muffins is being careful not to overmix the batter, which can overwork the gluten and yield dense, tough muffins.

What is the best way to store muffins?

I find the best way to store majority of muffins in any container covered but with a little bit of air circulation for the first 2 days. In many muffins mold can build up quickly if tightly closed. However, some muffins need tight seal storage to avoid from over drying. Store at room temperature on the counter. After, place in the fridge for 2-3 more days.

How do I freeze muffins?

Bake, cool completely and freeze leftover muffins in airtight container for up to 3 months. Thaw in the fridge overnight or on a counter for a few hours.

What is the best way to reheat them?

Pop muffin in a microwave, toaster oven or reheat in the oven at 350 F for 5-10 minutes.

Favorite Breakfast Healthy Muffins

Healthy Morning Glory Muffins

Combining dried fruits, nuts, and coconut flakes with oat or wheat bran, whole grain flour, maple syrup, and applesauce, these Healthy Morning Glory Muffins are made with wholesome ingredients, are low in sugar, and high in healthy fiber.

Healthy morning glory muffins studded with oats.

Healthy Oatmeal Muffins

Start your day off right with Healthy Oatmeal Muffins! Gluten free, vegan and refined sugar free, these protein packed healthy muffins are moist and delicious.

Healthy oatmeal muffins topped with oats in parchment paper liners.

Banana Protein Muffins

Banana Protein Muffins are moist, fluffy, and naturally sweetened. With 10 grams of protein, these healthy muffins makes a delicious breakfast or snack option.

Plus, you can even swap out the strawberries for other fruits based on what’s in season for a treat you can enjoy year round as a breakfast, post-workout, or mid-afternoon snack!

Banana protein muffins with raspberries and chocolate chips.

Carrot Oatmeal Muffins

Healthy Carrot Muffins made with applesauce, oats and maple syrup, and loaded with walnuts and raisins. Fluffy, light, moist and one of our top healthy muffin recipes!

Five healthy carrot cake muffins on white plate with raisins.

Protein Muffins

Easy, moist and fluffy Protein Muffins Recipe with 12 grams of protein and without the protein taste or bananas. Makes for a healthy grab-and-go breakfast or snack.

Protein muffins in a baking dish with chocolate chips and nut butter in a spoon.

Oat Bran Muffins

Oat Bran Muffins are tender, moist, and peppered with raisins, dates, and walnuts throughout. These healthy muffins are dairy free, naturally sweetened, and the perfect make ahead breakfast or snack!

View from top of oat bran muffins in muffin liners.

Healthy Muffins for Kids

Healthy Chocolate Chip Muffins

Healthy Chocolate Chip Muffins recipe made with whole wheat flour, no refined sugar and Greek yogurt are healthy bakery style muffins with lots of mini chocolate chips. It’s #1 of our healthy muffin recipes for kids.

Healthy chocolate chip muffins on cooling rack.

Healthy Banana Muffins

These Healthy Banana Muffins are the ultimate healthy banana treat. These healthy muffins rely on sweet overripe bananas and applesauce combined with whole wheat flour for a quick and simple breakfast or snack at just over 100 calories per muffin.

Healthy banana muffins in paper liners.

Healthy Chocolate Muffins

Healthy Chocolate Muffins with Greek yogurt, applesauce, whole wheat flour, cacao powder, and maple syrup are indulgently fudgy and loaded with chocolate chips. They’re so good, you’ll struggle to even allow them to cool down before they’re all gone!

Healthy chocolate muffins with chocolate chips on a counter.

Almond Flour Banana Muffins

Not only are these Almond Flour Banana Muffins naturally gluten-free, but they’re also low-carb, low sugar, grain-free, oil-free, and paleo-friendly! But you’d hardly be able to tell thanks to how fluffy, tender, and moist they are, with wonderfully sweet banana flavor.

Almond flour banana muffins stacked on top of each other with one showing texture inside.

Healthy Banana Chocolate Chip Muffins

Healthy Banana Chocolate Chip Muffins are moist, soft, and ready in 30 minutes. Packed with protein and potassium, yet without refined sugars, they deliver enough sweetness that kids still consider them a treat!

Healthy banana chocolate chip muffins with a bite taken out of.

Gluten Free Healthy Muffin Recipes

Oat Flour Banana Muffins

These Oat Flour Banana Muffins are soft, moist and loaded with banana flavor. They come together in one bowl and taste like a real deal!

Oat flour banana muffins on parchment paper and the one muffin cut and showing texture.

Almond Flour Zucchini Muffins

Almond Flour Zucchini Muffins are the perfect treat for summer! Naturally sweetened and naturally gluten free, they are perfect for packing on the go for a beach day, picnic or even after dinner treat.

Almond flour zucchini muffins stacked on top each other.

Almond Flour Blueberry Muffins

Healthy Almond Flour Blueberry Muffins are tender, fluffy and naturally gluten free! Made with almond flour, Greek yogurt, and sweetened with maple syrup they are perfect for a grab and go breakfast or snack.

Stack of almond flour blueberry muffins.

Almond Flour Yogurt Muffins

Almond Flour Yogurt Muffins are tender, moist, and fluffy with a light hint of lemon. Made with only 8 ingredients, these healthy muffins are also gluten free.

Almond flour yogurt muffins dusted with icing sugar and showing texture inside.

Healthy Lemon Poppy Seed Muffins

Healthy Lemon Poppy Seed Muffins are perfect anytime you need a light and flavorful muffin! Drizzle with a light lemon glaze for a brunch worthy item that is perfect for any weekend.

Healthy lemon poppy seed muffins with glaze and a slice of lemon on top.

Seasonal Healthy Muffin Recipes

Healthy Zucchini Muffins

Healthy Zucchini Muffins are easy to make in one bowl and super delicious! They are light, fluffy and moist muffins loaded with flecks of zucchini!

This means these healthy muffins replace the empty calories from white flour and sugar in regular muffins for a healthy, wholesome snack or breakfast.

Healthy zucchini muffins with a bowl of shredded zucchini nearby.

Healthy Pumpkin Muffins

These Healthy Pumpkin Muffins are low sugar, low fat and yet sweet and moist fall breakfast, afternoon snack or dessert. They are delicious and so easy to make!

Healthy pumpkin muffins on baking rack.

Healthy Strawberry Muffins

Bursting with berries, these whole grain Healthy Strawberry Muffins will be a new household favorite! Made with maple syrup, Greek yogurt, lower in sugar and low oil, makes these a muffin to feel good about.

Looking down at five healthy strawberry muffins on a platter.

Healthy Blueberry Muffins

While blueberry muffins are a classic, this version of Healthy Blueberry Muffins takes a healthy twist using whole wheat flour, maple syrup, applesauce, and plenty of fresh or frozen blueberries.

Healthy blueberry muffins on wood countertop.

Healthy Apple Muffins

These Healthy Apple Muffins are made with whole wheat flour, applesauce, grated apples and warm fall spices. Better yet, they are easy, moist and fluffy!

Healthy apple muffins with one muffin spread with butter.

Lemon Muffins

This easy Lemon Muffins Recipe has summer written all over it. Light, tangy, and perfectly moist, lemon muffins will brighten up any breakfast table or picnic.

Lemon muffins with a few slices of lemon served in a basket lined with towel.
healthy banana muffins

21 Healthy Muffin Recipes: Healthy Banana Muffins

Healthy Muffin Recipes including healthy banana muffins made with ripe bananas, applesauce, whole wheat flour, and no sugar. Made in one bowl and perfect for breakfast or snack.
5 from 1 vote
Servings 12 muffins
Calories 107
Prep Time 5 minutes
Cook Time 22 minutes
Total Time 27 minutes



  • Preheat oven to 375 degrees F and spray non-stick 12 muffin tin. Set aside.
  • In a large mixing bowl, gently whisk egg. Add bananas and mash. Add applesauce, maple syrup, oil, vanilla, baking powder and soda and salt; whisk to combine.
  • Add flour and gently stir until well incorporated. Do not over mix – that produces a tough muffin.
  • Fill each opening almost full with batter and bake for 22 minutes or until a toothpick inserted in the centre comes out clean.
  • Let muffins cool for about 5 minutes and then transfer to a cooling rack to cool off completely.



  • Store: Refrigerate in an airtight container for up to 1 week or freeze for up to 3 months.
  • Bananas. Choose very ripe bananas  – bruised bananas are even better! 
  • Flour. Do not use any other flour except what is listed. If you need gluten free – check out my almond flour banana muffins.
  • Liquid sweetener: You have to keep dry to wet ingredients ratio – use only liquid.
  • Sweetened or unsweetened applesauce. Can substitute with Greek yogurt 2% and higher fat content. 


Serving: 1muffin | Calories: 107kcal | Carbohydrates: 24g | Protein: 3g | Fat: 1g | Saturated Fat: 1g | Cholesterol: 14mg | Sodium: 179mg | Fiber: 2g | Sugar: 10g
Course: Muffins and Quick Bread
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. 5 stars
    I haven’t, yet, made any muffins, but I love all of your recipes and I can’t wait to try some of these. I will have to convert to mini muffins, because that’s the only pan I have. Thank you for so many great recipes.

  2. I quit making muffins because they always stick to the liners. Muffin pans are to hard to clean. Any tips on how to get the muffins out of the liners without tearing them apart?

5 from 1 vote

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