20+ of the Best Healthy Muffin Recipes for Clean Eating (2024)

These are some of the best healthy muffin recipes you can find for clean eating.

Homemade healthy muffins make a great snack or breakfast on the go. Whether your muffin of choice is banana muffins or blueberry muffins I’ve got you covered.

I love to keep things healthy and clean in the kitchen but also understand needing something quick and healthy for when you are short on time. These healthy muffin recipes work great for meal prep when you need to grab, heat and run. Having a great collection of the best healthy muffin recipes on hand makes snacking smooch easier.

Eating healthy does not mean that you have to sacrifice taste. Muffins are a great option for satisfying a sweet tooth for both kids and adults.

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Healthy Muffin Recipes for Clean Eating

When it comes to clean eating – muffins are my favorite. They are one of my all-time favorite snacks that I bake and keep on hand when I need a treat. You can easily adjust the healthy muffin recipes here and there to make a whole new flavor.

Another great thing about rotating through your healthy muffin recipes is that you can easily use them as part of your meal prep. Yep, freeze them and eat them as needed, whether as an afternoon clean eating snack or as a healthy breakfast muffin.

These muffin recipes are all made with simple clean ingredients. They are gluten free dairy free, refined sugar free but they are full of delicious flavor.

These are some of the best healthy muffin recipes you can find for clean eating. These easy healthy muffin recipes will make you want to make each and every one. We have a variety of vegan muffins, gluten free muffins, paleo muffins, blueberry muffins, banana muffins and even chocolate muffins. I know I'm about to be very busy in the kitchen making as many of these healthy muffin recipes as I can.

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Healthy Oatmeal Cinnamon Muffins

Healthy oatmeal cinnmon muffins. These delicous cinnamon oatmal muffins are gluten free,dairy free and vegan. They are the perfect balance of natural sweetness adn cinnamon.

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Healthy Blueberry Muffin Recipe

This gluten free healthy blueberry muffin recipe made with fresh blueberries and lemon comes out perfect every time, and make a great healthy snack.

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Healthier Chocolate Chip Muffins Recipe

These healthier chocolate chip muffins are moist and delicious. Healthy chocolate chip muffins make a great snack option or quick breakfast.

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Healthy Banana Muffins Recipe

Healthy banana muffins for the best moist muffins. This healthy banana muffin recipe make a great breakfast or snack. Moist, with sweet banana flavor and floral cardamom.

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Healthy Apple Muffins Recipe with Cinnamon

Healthy apple muffins are light, moist, and naturally sweet. This healthy apple muffin recipe makes the best healthy cinnamon apple muffins.

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Healthy Berry Oat Muffins Recipe

Healthy berry oat muffins make a great snack. These easy healthy mixed berry oatmeal muffins are delicious.

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Delicious Gluten Free Strawberry Banana Muffins

Healthy strawberry banana muffins recipe that is gluten free, refined sugar free and falls within a clean eating diet.

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Pumpkin Chocolate Chip Muffins Recipe

Fill the kitchen with the aroma of pumpkin with these healthy pumpkin chocolate chip muffins.

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Apple Oatmeal Muffins

When looking for healthy breakfast muffins these apple oatmeal muffins are sure to please. This oatmeal muffin recipe is packed with delicious apples, gluten free oats, and sweet bananas

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Healthy Strawberry Banana Muffins

healthy strawberry banana muffins are easy to make and naturally sweet with fresh strawberries and mashed banana,

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How to Make Healthy Chocolate Zucchini Muffins

These chocolate zucchini muffins are so light and moist. This healthy chocolate zucchini muffin recipe is packed with zucchini, healthy cacao and protein. Naturally sweetened with honey, they have no refined sugar, are gluten free, clean eating, and paleo.

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Healthy Chocolate Chip Pumpkin Muffins Recipe

These healthy chocolate chip pumpkin muffins are the perfect combination of chocolate, pumpkin spice, and walnuts.

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Healthy Blueberry Oatmeal Muffins Recipe

Healthy blueberry oatmeal muffins are deliciously moist and bursting with sweet blueberry flavor. Make the best healthy blueberry oat muffins.

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Blueberry Oat Muffins

This healthy blueberry oat muffins recipeis delicious and easy to make. Plus they store well so they makea great grab and go snack.

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Delicious Gluten Free Zucchini Bread Muffins

Thesegluten free zucchini bread muffins are so light and moist. They make a great afternoon treat, school snack, or quick breaskfast.

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How to Make Healthy Chocolate Chip Muffins with Walnuts

Healthy chocolate chip muffins with walnuts. This easy chocolate chip muffin recipe is gluten free, paleo and clean eating. Made without refined sugars they taste delicious.

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How to Make Delicious Gluten Free Chickpea Muffins

Chickpea muffins are packed with protein and glutamine. These healthy chickpea muffins make a great afternoon snack.

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How to Make the Best Healthy Banana Muffins

The best healthy banana muffin recipe that is sugar free and gluten free. These banana muffins made with applesauce are delicious.

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Banana Oatmeal Chocolate Chip Muffins

Photo Credit:www.katiebirdbakes.com

Banana Oatmeal Chocolate Chip Muffins: you would never believe that oats, bananas, and yogurt could together create something this amazing…until you try them. You can't go wrong with a healthy chocolate chip muffin recipe.

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Delicious and Easy Banana Nut Bread Muffins

Delicious and healthy banana nut bread muffins are easy to make. This banana nut bread recipe can be made into muffins or a loaf.

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Gluten Free and Paleo Beet Blueberry Muffins

Photo Credit:acleanbake.com

These kid-friendly muffins pack a (small) serving of vegetables, without differing in flavor or texture from a “normal” blueberry muffin. Made from wholesome ingredients and very lightly sweetened, this is a breakfast treat that will please kids and adults alike! I bet you never thought to add beets to your healthy blueberry muffin recipe before, did you?

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Rhubarb Almond Flour Muffins

Photo Credit:heartbeetkitchen.com

These rhubarb almond flour muffins are a true taste of spring! A gluten-free recipe, naturally sweetened with coconut sugar. No mixer required.

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Gluten Free Double Chocolate Chip Muffins - Sugar Free

Photo Credit:sunkissedkitchen.com

Gluten Free Double Chocolate Chip Muffins. These healthy chocolate muffins are entirely fruit sweetened, meaning they are an ideal breakfast treat!

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Healthy Banana Protein Muffins

Photo Credit:thecleaneatingcouple.com

These Healthy Banana Protein Muffins are the perfect nutritious breakfast! Gluten/dairy free and packed with protein, they're delicious + easy to make! These healthy banana chocolate chip muffins are one of my favorites.

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Gluten Free Strawberry Muffins | Paleo Muffins

Photo Credit:myculturedpalate.com

Gluten Free Strawberry Muffins. Berry muffins are light and tasty any time of day.

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Paleo Apple Cinnamon Muffins

Photo Credit:www.salads4lunch.com

These delicious Paleo Apple Cinnamon Muffins are the perfect way to start the day. They are a quick, grab and go breakfast recipe for busy weekday mornings but tasty enough as part of a weekend brunch. This healthy apple muffin recipe is sure to be a big hit!

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Carrot Muffins Recipe - Healthy Muffins

Photo Credit:myculturedpalate.com

Carrot muffins with raisins and nutsare one of my comfort foods. They are healthy muffins that don’t taste like it! Sweetened with honey and using clean ingredients, this healthy carrot muffin recipe is as good as it gets!

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Gluten-Free Cinnamon Flax Muffins

Photo Credit:www.cleaneatingkitchen.com

These Cinnamon Flax Muffins are gluten-free and vegan-friendly. They're grain-free and full of healthy fiber.

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Healthy Lemon Poppy Seed Muffins

Photo Credit:www.cleaneatingkitchen.com

These Healthy Lemon Poppy Seed Muffins are paleo and vegan, so they are grain-free, gluten-free, and dairy-free. Brighten up your day with this delicious clean eating muffins lemon treat.

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Double Chocolate Coconut Flour Muffins

Photo Credit:www.trialandeater.com

Double Chocolate Coconut Flour Muffins - naturally sweetened with no added sugar, and a paleo friendly snack. And, well, its chocolate!

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Gluten-Free Cherry Cobbler Muffins (Vegan, Oil-Free)

Photo Credit:www.moonandspoonandyum.com

These fluffy Gluten-Free Cherry Muffins have a soft, spongy and juicy cherry cobbler center! Made with a blend of buckwheat flour and tapioca flour, these delightful muffins are super quick and easy to make and filled with pleasing textures and flavors. Gluten-free, vegan, dairy-free, soy-free, nut-free and refined sugar-free

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Easy Vegan Protein Muffins (GF + Oil-Free)

Photo Credit:veganhuggs.com

These Vegan Protein muffins are quick, easy, healthy, and delicious! All you'll need is some common ingredients, a blender, muffin tin and your oven. (gluten-free & oil-free). You will love these vegan gluten free muffins, especially because you can customize them with all different toppings.

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Gluten Free Banana Muffin Recipe

Photo Credit:www.fearlessdining.com

Thisgluten free banana muffin recipeuses certified gluten free oats. Healthy dairy free, gluten free banana oatmeal muffins that taste so good, you will think they were a sweet treat.

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Strawberry Banana Chickpea Muffins (Gluten-Free)

Photo Credit:www.bucketlisttummy.com

Strawberry Banana Chickpea Muffins are light and fluffy, yet high in protein. These chickpea flour muffins aregluten-free and ready in 30 minutes. They are perfect for on-the-go snacks and kids.

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Gluten-free Bakery-Style Blueberry Muffins (egg-free + nut-free)

Photo Credit:rachlmansfield.com

Gluten-free Bakery-Style Blueberry Muffins made with all nut-free and egg-free ingredients for an easy and healthy blueberry muffin recipe.

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Vegan Sweet Potato Muffins (Fluffy & Gluten-Free)

Photo Credit:delightfuladventures.com

Fluffy, moist, and delicious gluten-freevegan sweet potato muffinsthat are loaded with mini chocolate chips and contain the perfect balance of warm spices.

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Vegan Gluten Free Morning Glory Muffins

Photo Credit:delightfuladventures.com

Healthy Vegan Gluten Free Morning Glory Muffins loaded with carrots, coconut, raisins, and apples. Perfect to have for breakfast or a snack.

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Baked Oatmeal Muffins with Cranberries

Photo Credit:www.veggieinspired.com

Baked Oatmeal Muffins w/ Cranberries - hearty and healthy, these delicious gluten free muffins will keep you satisfied all morning long. Perfectly portable if you're on-the-go. They make great lunchbox treats (they're nut free!) and after school snacks too!

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Paleo 5 Minute Muffins – Grain Free | No Added Sugars

Photo Credit:www.tessadomesticdiva.com

These lightening quick Paleo 5 minute healthy muffins are all done in the blender for a quick and nutritious muffin free of gluten and all grains. As an added bonus, there is no added sugar necessary!

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CHOCOLATE PROTEIN MUFFINS RECIPE

Photo Credit:laurengleisberg.com

I am always a fan of a protein muffin. Add chocolate and bananas to the mix and its a win-win.

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