11 Healthy Muffin Recipes

This article was written with help from AI and edited by Thrive Market’s talented team of human writers. 

Muffins are a culinary chameleon. Need a quick breakfast or mid-morning snack? Done. Something sweet (but not too sweet) for a baby shower or brunch? There’s a recipe for that too. Muffins can even stand in for dessert, especially when chocolate chips are involved. Our best recipes—like homemade blueberry muffins and tender pumpkin muffins—are crowd-pleasing for all ages and incorporate wholesome ingredients like whole-grain or gluten-free flours, alternative sweeteners, and secret additions like carrots and collagen for added nutrition. Plus, we’ve also rounded up tips for gluten-free baking, notes on how to turn any recipe into mini muffins, and the best ingredients from ThriveMarket.com to stock your pantry. 

11 Healthy Muffin Recipes

Start your ovens and bake up tasty and healthy muffins to enjoy throughout the week. Pro tip: Freeze any extras for speedy snacks whenever you need one.

Gluten-Free Blueberry Muffins

Tender, moist, and gluten-free, this batch of blueberry muffins is made with almond flour and ghee, plus a sweet burst from blueberries. 

Ingredients

2 cups almond flour
½ teaspoon sea salt
½ teaspoon baking soda
½ teaspoon ground cardamom
½ teaspoon ground cinnamon
2 organic large eggs
¼ cup melted ghee
⅓ cup raw honey
1 ½ teaspoons Madagascar vanilla extract
1 ¼ cup blueberries, plus more for the top
Pumpkin seeds
Baking cups

Instructions

Preheat oven to 350° F and line a muffin tin with paper liners.

In a large bowl, mix almond flour, baking soda, and salt.In a separate bowl, whisk together eggs, ghee, honey, and vanilla extract.Gradually fold the wet ingredients into the dry ingredients until combined, then gently stir in the blueberries.Divide batter evenly among the muffin cups.

Bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean.

Let cool before serving.

Blueberry and Turmeric Spice Muffins

No boring bran muffins here! We took easy blueberry muffins and spiced them up with turmeric, added pecans for extra crunch, and filled them with jam for a sweet surprise.

Ingredients

1 cup pecans
1 cup gluten-free rolled oats
⅔ cup buckwheat flour
1 ½ teaspoons baking powder
½ teaspoon baking soda
1 tablespoon turmeric
1 teaspoon cardamom
½ teaspoon ground ginger
½ teaspoon cinnamon
½ teaspoon sea salt
Pinch black pepper
⅔ cup yogurt
⅓ cup ghee
2 ripe bananas
5 Medjool dates
3 large eggs, beaten
1 cup blueberries
1 cup blueberry jam

Topping:
⅓ cup gluten-free rolled oats
2 tablespoons coconut oil
1 tablespoon honey

Instructions

Preheat oven to 400° F and grease a muffin pan with non-stick spray.

Add pecans and oats to a food processor and pulse several times to grind and create a coarse flour. Transfer mixture to a large mixing bowl and whisk together with buckwheat flour, baking powder, baking soda, turmeric, cardamom, ginger, cinnamon, salt, and pepper.

Add yogurt, ghee, bananas, and dates to the food processor and blend until smooth. Add this mixture along with the eggs to the dry ingredients. Fold to combine, then fold in blueberries.

Fill muffin cups halfway with batter, place 1 scant tablespoon of blueberry jam in the center, and top with batter to fill molds.

In a small bowl, quickly combine the ingredients for the topping and sprinkle on top of muffins.

Bake for 18 to 20 minutes. Let cool before removing from molds.

Collagen Mug Muffin

Here’s a single-serving muffin you can microwave in 2 minutes (really!) with a protein boost from collagen. 

Ingredients

1 scoop collagen peptides
2 tablespoons almond flour
1 tablespoon coconut flour
½ teaspoon ground cinnamon
¼ teaspoon baking powder
⅛ teaspoon salt
½ ripe banana, mashed
1 egg
1 tablespoon honey
1 tablespoon coconut oil, melted
1 tablespoon walnuts, chopped
1 tablespoon chocolate chips

Instructions

In a microwave-safe mug, mix almond flour, collagen peptides, baking powder, and salt.

Add the egg, mashed banana, and maple syrup (if using), and stir until smooth.

Microwave on high for 1-2 minutes, or until the muffin has set.

Let cool slightly before enjoying straight from the mug.

Gluten-Free Strawberry Oatmeal Cakes

We like to think of these oat-based bites as strawberry muffins that defy categorization. They’re also a gluten-free and vegan way to start your day. 

Ingredients:

3 cups gluten-free oats
1 tablespoon baking powder
½ teaspoon sea salt
2 teaspoon cinnamon
2 “flax eggs” (see below)
¼ cup maple syrup
2 teaspoons vanilla extract
½ cup unsweetened apple sauce (or strawberry for an extra-sweet take)
2 bananas, ripe
½ cup chopped strawberries

For one “flax egg”:
1 tablespoon flaxseed meal
3 tablespoons water

Instructions

Preheat oven to 350° F and grease a muffin tin.

In a large bowl, combine oats, almond milk, banana, maple syrup, vanilla extract, and cinnamon.

Fold in the diced strawberries.

Spoon mixture into the prepared muffin tin.

Bake for 25-30 minutes or until the tops are golden brown.

Let cool before serving.

Flourless Chocolate Zucchini Muffins

Everyone needs a zucchini muffin recipe for times when you can’t think of anything else to do with your summer crop. Moist and chocolaty, these flourless muffins sneak in zucchini for extra nutrition, making them a satisfying, anytime treat.

Ingredients

½ cup almond butter
1 ripe medium-sized banana
1 large egg
¼ cup raw honey
¼ cup cacao powder
2 tablespoons chia seeds
1 teaspoon vanilla extract
½ teaspoon baking soda
½ teaspoon sea salt
1 cup shredded zucchini, squeezed of excess liquid
Scant 1 cup dark chocolate chips, plus more for sprinkling on top

Instructions

Preheat oven to 350° F and line a muffin tin with paper liners.

In a large bowl, mix almond butter, zucchini, eggs, cocoa powder, baking soda, and honey until smooth.

Fold in chocolate chips, if using.

Divide batter among muffin cups.

Bake for 20-25 minutes or until a toothpick inserted into the center comes out clean.

Let cool before serving.

Chai Spiced Banana Crumb Muffins

These muffins bring together the flavors of three classic sweets: banana bread, crumb cakes, and chai lattes. The thick crumbly topping gets extra complexity of flavor from classic Indian spices like cardamom, ginger, and black pepper, while ripe bananas keep the batter delectably moist. Good luck stopping after just one.

Ingredients

For the crumb topping:
⅓ cup brown sugar
⅓ cup unbleached sugar
1 ½ teaspoon ground cinnamon
¾ teaspoon ground cardamom
1 ½ teaspoon ground ginger
Small pinch nutmeg
½ teaspoon freshly ground black pepper
⅛ teaspoon salt
½ cup coconut oil, melted
1 ¾ cups sprouted white wheat flour

For the batter:
⅓ cup Greek yogurt
1 large egg
1 large egg yolk
2 teaspoons vanilla extract
1 cup sprouted white wheat flour
½ cup unbleached sugar
½ teaspoon baking soda
½ teaspoon baking powder
¼ teaspoon salt
6 tablespoons coconut oil
2 to 3 extra-ripe bananas, sliced

Instructions

Preheat oven to 325° F and line a muffin tray with baking cups.

Make the crumb topping
Whisk brown sugar, unbleached sugar, cinnamon, cardamom, ginger, nutmeg, black pepper, and salt into melted coconut oil in a large bowl until smooth. Add flour with a spatula until mixture comes together as a solid dough. Press together in bottom of bowl and set aside.

Make the batter
In a small bowl, stir together yogurt, egg, egg yolk, and vanilla extract. Using a mixer fitted with the paddle attachment, mix together flour, sugar, baking soda, baking powder, and salt. Add coconut oil and a spoonful of yogurt mixture and mix on medium speed until flour is moistened. Add remaining yogurt mixture in two batches, beating for 20 seconds after each addition, and periodically scraping down the sides of bowl with a spatula.

Bake the muffins
Divide batter between 12 baking cups and arrange banana slices over top. Using your hands, break topping mixture into large crumbs and sprinkle over muffins. Bake cake until a tester inserted into center comes out clean, about 18 to 25 minutes. Cool completely before serving.

Pumpkin Muffin Recipe With Praline Topping

This easy pumpkin muffin recipe uses pantry staples. The muffins are topped with a sweet and crunchy praline topping for fall-inspired vibes.

Ingredients

For the muffins:
¼ cup almond milk, or milk of choice
½ teaspoon white vinegar or apple cider vinegar
1 cup flour (all purpose, whole wheat, or gluten-free)
⅓ cup coconut sugar
1 teaspoon baking powder
¼ teaspoon baking soda
¼ teaspoon ground ginger
¼ teaspoon ground nutmeg
¼ teaspoon sea salt
1 cup canned pumpkin
¼ cup virgin coconut oil, melted

For the praline topping:
¼ cup rolled oats
¼ cup walnuts, pecan halves, or raw almonds, chopped
1 tablespoon coconut sugar, optional
1 tablespoon coconut oil, melted
⅛ teaspoon sea salt

Instructions

Preheat oven to 350° F and line a muffin tin with paper liners.

In a bowl, whisk together pumpkin, eggs, brown sugar, oil, and vanilla.

In a separate bowl, combine flour, baking powder, baking soda, cinnamon, and nutmeg.

Gradually fold the dry ingredients into the wet ingredients until combined.

Spoon batter into muffin cups.

Mix pecans and brown sugar in a small bowl and sprinkle over each muffin.

Bake for 20-25 minutes or until a toothpick comes out clean.

Let cool before serving.

Easy Morning Glory Muffins

Originally created by Nantucket chef Pat McKinstry in the 1970s, this satisfying and healthy breakfast muffin packs carrots, raisins, walnuts, and sunflower seeds into every batch. 

Ingredients

3 large eggs, at room temperature
1 cup unsweetened vanilla almond milk
2 tablespoons melted coconut oil or ghee
1 package Simple Mills Banana Muffin Mix
1 teaspoon ground cinnamon
½ teaspoon ground ginger
3 large carrots, peeled and grated
½ cup raisins
2 cups roughly chopped walnuts
⅓ cup sunflower seeds

Instructions

Preheat oven to 350° F and line muffin tin with baking cups.

Whisk eggs, almond milk, and oil together in a large bowl. Add baking mix, cinnamon, and ginger and mix until thoroughly combined. Stir in carrots, raisins, walnuts, and sunflower seeds.

Divide batter between muffin cups and bake 25 to 30 minutes or until a toothpick inserted into the center comes out clean. Let cool completely before removing muffins from pan.

Egg and Spinach Breakfast Muffins

Leftover pancake mix makes easy work of these muffins filled with savory spices, eggs, cheese, spinach, and bacon. 

Ingredients

For the filling:
1 tablespoon extra virgin olive oil
1 medium yellow onion, chopped
3 cups fresh baby spinach

For the crust:
1 cup pancake and waffle mix
2 egg whites
1 egg
¼ cup milk
½ teaspoon onion powder
¼ teaspoon kosher salt
¼ teaspoon black pepper
½ cup shredded cheddar cheese

For the topping:
4 eggs, lightly beaten
½ teaspoon kosher salt
½ teaspoon black pepper
4 slices cooked bacon, chopped
¼ cup shredded cheddar cheese

Instructions

Preheat the oven to 350° F and line a muffin tin with baking cups.

Make the filling:
In a large skillet on medium-high heat, sauté onion for 5 to 7 minutes, until translucent. Add spinach and sauté until spinach has wilted, about 2 minutes. Remove from heat and set aside to cool.

Make the crust:
While the filling cooks, make the crust. In a medium bowl, add pancake mix, egg whites, whole egg, milk, onion powder, kosher salt, and pepper. Mix until combined, then stir in the cheese.

Make the topping:
In a medium bowl, beat eggs, salt, and pepper. Set aside.

Assemble the muffins:
Equally divide the crust mixture into 12 muffin liners, about 1 tablespoon in each. Follow with 1 heaping tablespoon of the vegetable filling, an equal sprinkling of chopped bacon, then 1 tablespoon of the egg topping. Sprinkle each muffin with 1 teaspoon of cheddar cheese on top. Bake for 10 to 12 minutes, until egg is set and slightly golden brown.

Morning Power Muffins

A little bit sweet, a little bit savory, this recipe is the perfect way to get some extra greens into your day. The batter gets rich flavor from salted caramel-flavored protein powder, but so can also swap in vanilla or chocolate too.

Ingredients

2 cups spinach
1 ripe banana
1 cup apple sauce
1 ½ cups unsweetened almond milk
½ cup brown sugar
¼ cup coconut oil, melted
1 ½ teaspoons vanilla extract
1 ½ cup almond flour
1 cup coconut flour
½ cup tapioca flour
2 scoops Vega Protein and Greens, Salted Caramel
1 teaspoon baking powder
1 teaspoon baking soda
1 teaspoon ground cinnamon
½ teaspoon ground nutmeg
1 teaspoon sea salt

Instructions

Preheat oven to 350° F and line a muffin tin with liners. Pulse spinach a few times in a food processor, then add banana, apple sauce, almond milk, brown sugar, coconut oil, and vanilla; process until well blended.

Add remaining ingredients a large bowl; whisk. Add wet ingredients and stir until combined. Portion batter into prepared muffin tin.

Bake 25 to 30 minutes, or until a toothpick inserted in the center of a muffin comes out clean. Cool muffins completely. Refrigerate in an airtight container for up to 3 days.

Paleo-Friendly Cacao and Cold Brew Muffins

Perk up your morning with a paleo-friendly breakfast made with a robust cold brew. 

Ingredients

4 eggs
⅓ cup Califia Farms Cold Brew
3 tablespoons coconut oil or vegetable oil
3 tablespoons maple syrup
1 tablespoon vanilla extract
1 box Simple Mills Almond Flour Pancake & Waffle Mix
¼ cup cacao powder
½ cup toasted walnuts, chopped

Instructions

Heat oven to 350° F and mist a muffin tin with cooking spray. Whisk eggs, cold brew, oil, maple syrup, and vanilla in a large bowl. Add the baking mix and cacao powder; whisk until well blended. Fold in half of the walnuts, then divide batter evenly between the muffin cups, filling them about ⅔ of the way full. Sprinkle remaining walnuts on top. Bake for 15 to 20 minutes, or until a toothpick comes out clean. Cool completely. 

Tips for Making Gluten-Free Muffins

Looking for the perfect texture and flavor with gluten-free ingredients? Follow these tips for a reliable bake every time. 

• Choose the right flour blend. There’s a lot to explore in gluten-free baking, and it may take some trial and error to find your favorite mix of alternative flours. Almond, coconut, and even pre-mixed options all have unique flavor profiles and textures that will impact your final recipe. Our favorite approach? Stay curious and don’t give up. 
• Measure by weight. Baking is more science than art, and when working with gluten-free flours, it helps to be extra precise. Invest in a kitchen scale to measure your ingredients for complete accuracy. 
• Mix well. With traditional baked goods, overmixing can result in dense textures because overdeveloped gluten is to blame. It’s not an issue when baking gluten-free, and in some cases, ingredients may need to be mixed more. 
• Add a binding agent. Gluten-free flours don’t have the same elasticity as their traditional counterparts. If not using a pre-mixed GF flour blend, consider adding a binding agent like xanthan gum to help your dough hold together.  
• Keep pre-made mixes in the pantry. When you’re short on time or are running low on gluten-free flours, just open up a bag of pre-mixed dry ingredients. Whip up easy apple muffins or healthy banana muffins in no time.

Tips for Making Mini Muffins

Looking to turn your muffin recipe into a bite-sized version? Here are some tips to help them turn out well. 

• Adjust your baking time.  Mini muffins bake much faster than standard muffins, so check for doneness at 10-12 minutes.
• Grease or line the pan: Mini muffins are more prone to sticking, so use non-stick spray or mini liners. 
• Use a small scoop: To evenly distribute the batter, use a small cookie scoop or spoon. 
• Don’t overfill. Fill each mini muffin cup about ¾ full to avoid overflow. 
• Experiment with toppings: Add mini chocolate chips, a sprinkle of cinnamon sugar, or a dollop of jam to each muffin for variety. 
• Cool thoroughly: Let the muffins cool completely in the pan before attempting to remove them.

Best Baking Products from Thrive Market

Enhance your baking experience with these top-quality products available at Thrive Market:

Bob’s Red Mill Baking Powder

Baking powder is a must-have to make muffins rise, and according to Thrive Market member Sarah from Texas, “this baking powder works great in all my recipes. I love that it’s aluminum-free!” 

Thrive Market Chocolate Chips

Sweetened with stevia, this keto-friendly pick is made with ethically sourced, 55% cacao from Colombia. Gladys from New Jersey shares “I ordered these to make some chickpea brownies and or cookies and they’re delicious!”

Thrive Market Blanched Almond Flour

New to your gluten-free baking journey? A bag of almond flour is a great place to start. Kelly from New York loves the texture and Melinda from California says “this almond flour makes the best cookies!”

Thrive Market Organic Pure Vanilla Extract

There’s nothing quite like the mellow flavor of vanilla. This is sourced directly from farmers in Madagascar and packaged in an eco-friendly bottle. Ann from Indiana says it’s “excellent quality and delicious in baked goods.”

Thrive Market Organic Maple Syrup

Sourced from maple trees in Vermont, this rich syrup adds sweetness to your baked goods. Member Rachel from Boston, MA says “this maple syrup is my go-to for baking and breakfast. The flavor is outstanding!”