Best Healthy Muffin Recipes from The Muffin Queen

That’s right, this Muffin Queen (hi, it’s me!) rounded up my favorite healthy muffin recipes that are perfect for breakfast, snacks, desserts, and especially sharing with the people you love. LET’S DO IT UP PEOPLE.

When I first shared this roundup a couple of years back I only had about 30 muffins recipes, but now we’re just over 50 (and you know there are plenty more to come). Truth: I call baking my therapy. When I’m feeling anxious, I trash up my kitchen and bake my heart out. It soothes the soul.

But you know what I love even more? Baking for the ones I love. There’s nothing better than expressing your love and gratitude for someone than with freshly baked goodies.

How to freeze muffins

All of these wonderful muffin recipes are freezer-friendly! Simply wrap muffins individually in freezer-safe bags or store them in a large freezer bag. When you’re ready to enjoy them, reheat for 30-45 seconds in the microwave or simply thaw them at room temperature.

two blueberry zucchini muffins in a stack

Our fav tools for baking muffins

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Each of these healthy muffin recipes has a unique flavor and add-ins, but they all have one thing in common…they are amazingly fluffy, perfectly sweet and have wholesome ingredients. I created these recipes using different flours so that there’s a good mix of regular and gluten-free that you can share with anyone.

I separated all of these muffins into different flavors for easy scrolling. Yes, many of them overlap because I love to combine lots of flavors together, but you’ll get the gist! I also included oatmeal muffin cups because they’re so cute and muffin-like. BEST breakfast. Enjoy!

GF = gluten free

healthy banana muffins on a board with walnuts

Banana Muffins

Honey Cinnamon Walnut Banana Muffins

Healthy Double Chocolate Banana Muffins

Paleo Double Chocolate Tahini Banana Muffins GF

Healthy Peanut Butter Banana Muffins GF

Skinny Banana Chocolate Chip Muffins

Power Flax Chocolate Chip Banana Oatmeal Muffins

Vegan Paleo Banana Muffins with Chocolate Chips GF

Flax Almond Meal Banana Muffins with Dark Chocolate (gluten free, paleo!)

Healthy Gluten Free Banana Muffins GF

almond butter peach blueberry baked oatmeal cups on a wooden board

Oatmeal Cups & Muffins

Carrot Cake Baked Oatmeal Cups GF

Almond Butter Peach Blueberry Oatmeal Cups GF

Chai-Spiced Healthy Apple Oatmeal Muffins

Peanut Butter Banana Baked Oatmeal Cups GF

Almond Butter Apple Cinnamon Baked Oatmeal Cups GF

Baked Pumpkin Chocolate Chip Oatmeal Cups GF

healthy zucchini muffins on a wire rack

Zucchini Muffins

Heart Healthy Olive Oil Salted Chocolate Chip Zucchini Muffins GF

Healthy Double Chocolate Zucchini Muffins

Morning Glory Zucchini Carrot Muffins GF

Chunky Monkey Zucchini Banana Muffins

Chia, Lemon & Strawberry Zucchini Muffins

Good Morning Healthy Maple Blueberry Zucchini Muffins

Paleo Banana Zucchini Muffins GF

bakery style blueberry muffin on a plate with blueberries

Berry Muffins

The Best Bakery Style Blueberry Muffins You’ll Ever Eat

Strawberry Kissed Almond Butter Muffins GF

Healthier Blueberry Greek Yogurt Muffins

Raspberry, Almond Butter & Banana Oatmeal Muffins

Blackberry Peach Oat Bran Muffins with Chia + Flax GF

The Best Healthy Blueberry Oatmeal Muffins GF

chocolate pumpkin muffins in a stack

Pumpkin & Sweet Potato Muffins

Nourishing Almond Butter Double Chocolate Pumpkin Muffins (that taste like CAKE!) GF

Pumpkin Zucchini Muffins with Cinnamon Cream Cheese Frosting

Brown Butter Orange Pumpkin Muffins with Orange Glaze

Healthy Chocolate Chip Sweet Potato Muffins

Healthy Pumpkin Banana Muffins with Macadamia Nut Crunch

Healthy Marbled Chocolate Pumpkin Muffins

Chai-Spiced Pumpkin Oatmeal Muffins with Vanilla Bean Cream Cheese Glaze

Healthy Pumpkin Chocolate Chip Muffins

Pumpkin Chocolate Chip Oat Protein Muffins

Whole Wheat Pumpkin Chocolate Chip Muffins (made with greek yogurt!)

banana spinach muffins on a wire rack

Sneaky Veggie Muffins

Blender Banana Spinach Muffins (kid-friendly!) GF

Healthy Carrot Cake Muffins with Cream Cheese Glaze

Blender Double Chocolate Spinach Muffins GF

bacon egg muffin cups with avocado cubes on a plate with a fork

Savory Muffins

Mushroom Spinach Bacon Egg Cups (low carb!) GF

Healthy Breakfast Egg Muffin Cups GF

Savory Chicken Sausage, Egg and Cheese Muffins (keto + low carb) GF

Loaded Veggie Avocado Quinoa Frittatas GF

lemon poppy seed muffin with blueberry glaze

Citrus Muffins

Healthy Lemon Poppy Seed Muffins with Lemon Blueberry Glaze

Dreamy Orange Chocolate Chip Muffins

gluten free cornbread muffins on a wire rack

Cornbread Muffins

Gluten Free Cornbread Muffins GF

Healthy Blueberry Zucchini Cornbread Muffins

Healthy Maple Sweet Potato Cornbread Muffins GF

healthy bran muffin with a bite taken out

Classic Muffins

Grandma’s Healthy Bran Muffins

Healthy Gluten Free Chocolate Chip Muffins GF

Healthy Gingerbread Muffins

top-down view of a chickpea muffin

Unique Muffin Recipes

Fluffy Flourless Peanut Butter Chickpea Muffins GF

Flourless Black Bean Brownie Muffins GF

Vegan & Gluten Free Pistachio Muffins with Strawberry Cream Cheese Glaze GF

If you make any of these muffin recipes be sure to leave a comment and a rating on the recipe so I know how you liked it!

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