If you’ve spent any time exploring my website, then you know how much I love creating healthy muffin recipes. I have more than thirty (!!) different muffin recipes on my site, and I love each for its own delicious reasons. Today, I’m sharing the The BEST Healthy Muffin Recipes and How to Store Them.

Blender Banana Oatmeal Muffins topped with chocolate chips

Since my full list of healthy muffin recipes (let alone my breakfast recipes), is quite, erm, extensive, in today’s post, I’m organizing these the muffins into helpful categories like low calorie healthy breakfast muffins, healthy blueberry muffin recipes, healthy muffin recipes with vegetables, and more! You can even find healthy breakfast muffin recipes without sugar (the refined kind).

Whatever your muffin motivation, you’ll find just the recipe to meet your needs.

Need quick, easy, and delicious breakfasts, snacks, or desserts? These muffins are the answer. They’re perfect for packing in lunchboxes and taking with you on the go.

With all of my healthy muffin recipes, I’ve made it my goal to use wholesome ingredients, make healthy swaps wherever possible, and create the most tasty muffin possible. I know you’ll find one (or multiple!) recipe that the entire family will love.

A muffin pan with banana muffins

Healthy Muffin Recipes

Click on any of the below to jump quickly to that category. For my best healthy muffin tips, read on.

Are Muffins Healthy?

Yes! If eaten in moderation and free from processed ingredients, muffins can be healthy.

  • When looking for healthy muffin recipes, try to find ones with wholesome ingredients, filling fiber or protein, and less sugar.
  • MANY muffins are closer to a cupcake, especially the ones sold in bakeries and grocery stores. These store-bought muffins can be filled with lots of calories, excess fats and oils, refined sugars, and typically lack the fiber necessary to keep you full.
  • While it’s fine to indulge every now and then, if your goal is finding a healthy breakfast, then you want to make sure you are making a good choice.

Fortunately, you can enjoy muffins that taste great AND are made of healthy ingredients too!

All of the muffins on this list are moist and flavorful, and are made without refined sugar, and they include nutrient-dense ingredients like fruits or vegetables. Many of the recipes below utilize filling and healthy ingredients like oatmeal or banana to ensure that you actually feel satisfied after enjoying them.

If you’re worried about the calorie count, try making one of these muffin recipes in a mini muffin pan, so each muffin will contain less calories. Plus, you can freeze a batch, and thaw them one at a time for quick and easy breakfasts or snacks.

How to Store and Freeze Healthy Muffins

  • To Store. Place muffins in an airtight storage container lined with paper towel for up to 5 days.
  • To Freeze. Store muffins in an airtight freezer-safe storage container or ziptop bag in the freezer for up to 3 months.
  • For even more tips on how to store and freeze muffins, check out my guide on how to store muffins.

What to Serve with Healthy Muffins

Because these muffins are made with whole grains, they are higher in fiber, and thus more filling. If you’d like to make them a part of a larger breakfast spread, here are a few ideas.

  • Bacon. If you’re serving healthy muffins for breakfast, a side of Baked Bacon and
  • Breakfast Casserole. Serve a hearty and filling breakfast by pairing muffins with a breakfast casserole like Whole30 Breakfast Casserole, Healthy Breakfast Egg Muffins, or Crockpot Egg Casserole.
  • Smoothies. Start the day on the right foot with healthy muffins and any of these Healthy Breakfast Smoothies.
  • Fruit. For a healthy snack, breakfast, or dessert serve muffins with a side of fresh fruit or these kid-friendly Healthy Peanut Butter Yogurt Fruit Pizzas.
  • Almond Butter or Peanut Butter. Two of my favorite things to spread over muffins. Warm up the muffin first to make it even more wonderful.
  • Greek Yogurt. My favorite muffin combo is nut butter AND Greek yogurt. Try adding a dollop of both. So yummy and filling!

Now that we’ve chatted over the basics, let’s dive into those healthy muffin recipes!

Healthy Oatmeal Muffin Recipes

The BEST Healthy Blueberry Muffins – moist and fluffy with blueberries in every bite! Made with whole wheat flour, applesauce. Recipe at wellplated.com | @wellplated

These muffins contain oatmeal, which is a powerhouse ingredient for fiber and protein. They will keep you full for hours!

Healthy Banana Muffins

white plate full of healthy banana muffins surrounded by walnut pieces

Readers RAVE about my banana muffins! They’re incredibly moist, easy, and so much better for you than the store-bought kind.

Healthy Protein Breakfast Muffins

A muffin tin filled with homemade muffins

If you’re looking for filling protein to fuel you, these are the muffins for you! Each one is packed with protein-rich ingredients to keep you energized.

Muffins with Hidden Veggies

muffin pan full of Chocolate Chip Banana Healthy Zucchini Muffins

Whether you’re trying to add more veggies to your diet or sneak a few into your kid’s diet, these muffins will do the trick! These muffins are all delicious, and you won’t even notice the veggies.

Healthy Pumpkin Muffins

A muffin pan filled with almond flour pumpkin muffins

A classic fall ingredient makes these healthy muffins incredibly moist. These recipes are perfectly spiced. We love to enjoy these pumpkin muffins year-round!

Healthy Muffin Recipes for Kids

A delicious and healthy recipe for Applesauce Muffins with oatmeal, cinnamon, and honey. Healthy, tasty muffins with no sugar and no butter! The perfect healthy muffins for kids and grown-ups too!

Kids love the flavors of these muffins, and they’re easy to eat. They’re the perfect size for a snack or easy dessert!

Chocolate Muffin Recipes

Double Chocolate Banana Muffins made with whole wheat and chocolate chips

The more decadent side of my healthy muffin recipes! These chocolate muffins are ultra rich and chocolatey while still containing tons of healthy ingredients.

Unique Muffin Recipes

Irish Soda Bread Muffins – like traditional Irish soda bread, but easier to make (and eat!). Buttery, moist muffins, perfect for St. Patrick’s Day or a healthy breakfast year-round. Recipe at wellplated.com | @wellplated

These are muffin recipes you won’t find at the store. Unique ingredients come together to create incredibly delicious flavor!

What’s YOUR favorite muffin recipe? Whether it’s on this list or not, I’d love to hear about it in the comments below! I love hearing from you, and I’m always looking for new ideas.

Did you try this recipe?

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at wellplated.com and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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  1. We love muffins – just saying! In the past I’ve commented on your method of storing muffins – it’s the best I’ve tried. Many times using an ice cream scoop just doesn’t work but I found some REALLY neat scoops at Bed, Bath and Beyond that pick up the slack. They’re only $5.99 and with a coupon, they’re less. They come in 3 sizes – jumbo, regular and mini. They also have a silicone edge so that you can get the last little bit of batter from the bowl. A great tool find !