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Home » Recipes » Best Of

Healthy Muffin Recipes for Breakfast

By Laura Fuentes Updated Jun 4, 2025

5 from 10 votes

Recipe

This post may contain affiliate links. Read our disclosure policy here.

Grab one of these 10 healthy muffin recipes that are perfect for breakfast any day of the week!

Love muffins for breakfast? My kids do too! Below, you’ll find muffin recipes with nutritious add-ins, fruit, and whole grains that make it easy to make breakfast the most favorite meal of the day!

an image collage of healthy muffin recipes for breakfast

Can Muffins Be Healthy?

Muffins can be a healthy breakfast option, especially when they’re made at home with nutritious and simple pantry-staple ingredients. Some reasons the recipes below are considered healthier than other breakfast options are because they…  

Include Oats and Oat Flour
Oats are nutritious and can be made into oat flour. They’re better than regular flour and have a lower glycemic index so muffins made with them are a great option.

Reduce Fats
A great way to make muffins moist and reduce the fat content is to use Greek yogurt, mashed bananas, or pumpkin pureé.

Add Nutritious Ingredients
While everyone loves a great chocolate chip muffin, other add-ins that provide nutritional value include flax meal, chia seeds, dried fruits, raisins, fresh or frozen berries, yogurt (protein), and more. 

Limit Refined Sugars
In many recipes, granulated sugar can be substituted for honey, which is less refined than white sugar. Others have reduced amounts and are naturally sweetened with bananas.

Use Alternative Flours
Consider trying some of the muffin recipes made with coconut or almond flour for a delicious and nutritious breakfast boost!

Healthy Breakfast Muffin Recipes

Try one of the recipes below for a healthy and delicious breakfast muffin that will be devoured by kids and adults alike. Enjoy them fresh or bake a batch, freeze, and warm up when you want one!

overhead view of muffins on a cooling rack
Blueberry Muffins
4.88 from 33 votes
100% delicious with just half the amount of butter than the classic recipe.
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four paleo muffins
Almond Flour Pancake Muffins
5 from 26 votes
Packed with nutrition and plenty of delicious in every bite.
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Banana Oatmeal Muffins
Think banana oatmeal but in muffin form thanks to an easy-to-make batter in the blender!
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a few muffins on a cooling rack on the side
Strawberry Yogurt Muffins
4.88 from 50 votes
These can be made with fresh or frozen strawberries and include extra protein from the yogurt in the batter.
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Oatmeal Muffins
These muffins are hearty, delicious, and filling all with the taste that both kids and adults love.
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One muffin in a tin lunchbox with halved boiled egg and grape tomatoes
Healthy Morning Glory Muffins
5 from 32 votes
Made with coconut flour, flax meal, and filled with veggies, these muffins are naturally sweet and delicious too!
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Lemon Poppyseed Muffins
Super moist muffins with grated zucchini, oats, zesty lemon, and poppy seeds have that bakery-style feel but made at home.
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apple cinnamon muffins
Apple Fritter Muffins
5 from 19 votes
Say goodbye to fried fritters. These muffins have bits of apples and cinnamon baked inside.
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Cheddar Apple Sausage Muffins
These savory muffins include oats, sausage, apple, and spinach for an on-the-go breakfast combo!
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two pancake muffins on a plate
Chocolate Chip Pancake Muffins
5 from 17 votes
Portion controlled muffins that taste like pancakes without the need to pour syrup on top!
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How to Pre-Ahead Muffins for Easier Mornings

I love making the muffin batter the night before so all I have to do is stick the muffin pan in the oven in the morning and everyone can enjoy fresh out-of-the-oven muffins!

You can do this by making the batter as directed in the recipe the night before, cover the bowl, and keep it in the fridge overnight. In the morning, remove the batter from the fridge and let it come to room temperature while the oven preheats, fill the muffin pan, and bake!

For the ultimate convenience, you can also freeze the muffin batter for up to 2 months inside muffin liner cups. All you do is thaw, bake, and enjoy. It can be that easy!

Healthy Muffin Recipes for Breakfast

an image collage of healthy muffin recipes for breakfast
Servings: 8 muffins
Prep Time: 10 minutes mins
Cook Time: 22 minutes mins
Grab one of these 10 healthy muffin recipes that are perfect for breakfast any day of the week!
5 from 10 votes
Print Pin

Ingredients

  • ½ cup flax meal
  • ¼ cup walnuts
  • 1 tablespoon coconut flour
  • ¼ teaspoon baking soda
  • ¼ teaspoon salt
  • ½ teaspoon cinnamon
  • ½ cup raisins
  • 3 large eggs
  • 2 tablespoons coconut oil (or butter), melted
  • ¼ cup grated carrot, about 1 large carrot

Instructions

Prep:

  • Preheat oven to 350F and line 8 muffin cups with paper liners.

Make the batter:

  • In a food processor, combine flax meal, walnuts, and coconut flour until it resembles coarse sand. Add baking soda, salt, and cinnamon; pulse a few times to combine. Add raisins and pulse, until they are chopped and incorporated into mixture (you are not trying to make a paste, just a coarse dough of sorts).
  • Add eggs and melted coconut oil or butter and pulse a few times to incorporate. Fold in grated carrot just to combine. Spoon in about ¼ cup of muffin batter into prepared muffin cups.

Bake:

  • Bake for 22 minutes, or until a toothpick comes out clean when inserted in the middle. Allow muffins to fully cool before eating them.

Equipment

Clean Treats
Clean Treats Cookbook
batter bowl with a lid
Batter Bowl with Lid

Nutrition

Serving: 1 muffin | Calories: 179kcal | Carbohydrates: 14.1g | Protein: 5.5g | Fat: 12.1g | Saturated Fat: 4.1g | Cholesterol: 69.8mg | Sodium: 154.7mg | Fiber: 4.3g | Sugar: 7.4g

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Comments

    5 from 10 votes (6 ratings without comment)

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    Recipe Rating




  1. Hayley says

    May 21, 2024 at 7:27 am

    5 stars
    I love these healthy muffin recipes! It’s great that I can choose from so many, I never get bored, thank you!

    Reply
  2. Anya says

    May 10, 2024 at 2:57 pm

    5 stars
    So many delicious muffin recipes! I want to bake them all!

    Reply
  3. Terry says

    May 01, 2024 at 3:18 pm

    5 stars
    Muffins can be healthy!!!!! My mind is blown this is not clickbait. Laura is awesome at explaining food and the reason why things are healthy for you.

    Reply
  4. Adeline says

    April 29, 2024 at 9:32 pm

    5 stars
    Such a great variety to choose from. I am always looking for a healthy muffin recipe, saving all of these!

    Reply

Hi! I'm Laura.
Certified Integrative Nutrition Health Coach, mom of three, and the woman behind the world’s best pancakes—here to help you ditch the mealtime drama with recipes your family will actually eat.

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