10 Healthy Muffin Recipes

These healthy muffin recipes include blueberry muffins, banana muffins & more! Made with wholesome ingredients, they're moist, fluffy, and delicious.

healthy muffin recipes

The next time you’re in the mood for an easy baking project, roll up your sleeves and try one of these healthy muffin recipes! They include a recipe for every classic muffin you can think of – blueberry, banana, zucchini, chocolate chip, and more – but they’re all made with wholesome ingredients like whole wheat flour, almond flour, Greek yogurt, and maple syrup. Still, they deliver everything you want in a muffin, healthy or otherwise. They’re moist, tender, puffy, and lightly sweet. Two (or three) for me, please!

Before you get to baking, here’s a tip: all these healthy muffin recipes freeze perfectly. I like to make a double batch and enjoy one or two right away. Then, I freeze the extras. They’ll keep for up to 3 months in the freezer, and I love to have them on hand for a quick, comforting breakfast or snack. To thaw one, just pop it in the microwave for about 30 seconds. Now…to the recipes!

Very Berry Healthy Muffin Recipes

Swap in frozen berries when fresh ones are out of season.

Healthy Blueberry Muffins

Blueberry Muffins
These healthy muffins aren’t the jumbo, super-sweet treats you might imagine when you think of blueberry muffins. Instead, they’re small, soft, and puffy, perfect for breakfast or a snack.

Healthy muffin recipes - strawberry muffins

Strawberry Muffins
These muffins are some of my favorites on this list! Sweet, juicy strawberries fill every bite.

Extra-Moist and Tender Muffins

Ok, to be clear, all of these muffins are tender and moist. But these two healthy muffin recipes are especially so, thanks to the help of two key ingredients: banana and zucchini.

Healthy Banana Muffins

Healthy Banana Muffins
Love banana bread? Then you’ll flip for these healthy muffins! They’re amazingly moist, sweet, and packed with spiced banana flavor. Use a flax egg to make them vegan.

zucchini muffins

Zucchini Muffins
The best way to eat your veggies! These healthy muffins are a hit with both kids and adults.

Healthy Muffin Recipes for Chocolate Lovers

Chocolate for breakfast? Yes, please!

Healthy muffin recipes - Chocolate chip muffins

Chocolate Chip Muffins
Many bakery-style chocolate chip muffin recipes call for sour cream. Here, I replace it with a healthier swap: Greek yogurt! It gives the muffins a delicious moist texture and helps them puff up as they bake.

Chocolate zucchini muffins

Double Chocolate Zucchini Muffins, page 269 of The Love & Lemons Cookbook
To make these ultra-chocolatey muffins, you’ll mix cocoa powder into the batter and fold in chocolate chips. So what makes them healthy (ok, healthy-ish)? Whole wheat flour, pure maple syrup, and, of course, zucchini!

Warm and Cozy Muffins

These healthy muffin recipes are my go-tos throughout the fall and winter. I love to make them on chilly mornings, when nothing sounds better than warming up with a freshly baked muffin and a hot cup of coffee or tea.

Apple Cinnamon Muffins

Apple Cinnamon Oat Muffins, page 57 of Love & Lemons Every Day
I make these muffins with a mix of oat flour, almond flour, and arrowroot starch, which makes them super soft and tender…and totally gluten-free!

Healthy pumpkin muffins recipe

Pumpkin Muffins
Pumpkin spice lovers, this one’s for you! The pumpkin puree gives these muffins a perfect moist and fluffy texture.

Bright and Zesty Healthy Muffin Recipes

Break out the lemons and limes! These healthy muffin recipes are bright and fresh.

Healthy muffin recipes - vegan lemon muffins

Vegan Lemon Muffins
We all love lemon poppyseed muffins, but I’d like to make the case for these lemon chia seed muffins, too. They’re bright and flavorful, thanks to Meyer lemon juice and zest, and the chia seeds add a delicious, delicate crunch. Serve them with a cold glass of almond milk for crave-worthy breakfast or snack!

Healthy muffin recipes - Mango Coconut Muffins

Mango Coconut Muffins
These vegan muffins are bursting with the flavors of mango, coconut, and lime. We love to make them for a fun, fresh breakfast treat.

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Healthy Muffin Recipes: Blueberry Muffins

rate this recipe:
5 from 8 votes
Prep Time: 10 minutes
Cook Time: 17 minutes
Total Time: 27 minutes
Serves 12
These blueberry muffins are one of our favorite healthy muffin recipes!



  • Preheat the oven to 400°F and grease a 12-cup muffin tin.
  • In a medium bowl, combine the whole wheat and almond flours, the baking powder, cinnamon, and salt.
  • In a large bowl, vigorously whisk together the almond milk, olive oil, eggs, sugar, vanilla, and lemon oil, if using.
  • Dust the blueberries with ½ teaspoon flour and toss to lightly coat them. This will prevent them from sinking to the bottom of the muffin cups.
  • Pour the dry ingredients into the wet ingredients and stir to combine. Gently fold in the blueberries. Use a ⅓-cup measuring cup to scoop the batter into the muffin cups. Bake for 17 minutes, or until the muffin tops spring back to the touch.


*Or a 50/50 mix of all-purpose and whole wheat flour.


5 from 8 votes (7 ratings without comment)

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Rate this recipe (after making it)

  1. Chequeta Nutt

    which cookbook would have the most of the healthy muffins?

    • Phoebe Moore (L&L Recipe Developer)

      Hi, each of the Love & Lemons cookbooks has one healthy muffin recipe in it. The rest of these are on the blog!

  2. Alexandra

    I’m new to your site. Will be trying the radish pesto tonight! But I’m really wondering if there is nutritional info for the recipes. I’d like to try the muffin recipes. Maybe I’m just missing it.

    • Jeanine Donofrio

      Hi Alexandra, I hope you enjoy the pesto! I don’t post nutrition facts, but you could plug the ingredients into a site like my fitness pal.

  3. Helen

    Hello, I was wondering if you have the nutrition info on these please,

  4. Ann

    Hello! I’d like to bake these muffin, however, we need to make them nut free. Do you recommend another flower instead of the almond flower? Or to just substitute it with more whole wheat flower? Thank you!

  5. susan wright

    Does flax egg always work to replace eggs, when substituting to make it a vegan option.?
    Also, does coconut sugar, maple syrup, or Stevia Make for a decent white sugar substitute?
    Thank you for your beautiful, easy, flavorful recipes.

    • Jeanine Donofrio

      Hi Susan, flax eggs don’t always work, so I would stick to the recipes where we’ve used flax on the recipe or listed it in the notes section as a vegan option – those have been tested with successfully with flax.

      You can substitute coconut sugar for granulated sugar. I wouldn’t use maple syrup in place of granulated sugar because it changes thee wet to dry ratio. For stevia, I would google for recipes that specifically use stevia, I wouldn’t replace it 1:1 for sugar because the texture is completely different.

      Hope that helps!

    • Brittany R

      5 stars
      I substituted both eggs for 1 unsweetened applesauce and didn’t put the sugar at all. Turned out amazing! (also used regular whole wheat instead of pastry flour.) However, I don’t like things super sweet to begin with.
      Thinking about adding some banana to my next batch.

A food blog with fresh, zesty recipes.
Photograph of Jeanine Donofrio and Jack Mathews in their kitchen

Hello, we're Jeanine and Jack.

We love to eat, travel, cook, and eat some more! We create & photograph vegetarian recipes from our home in Chicago, while our shiba pups eat the kale stems that fall on the kitchen floor.