A collection of delicious, dietitian-approved healthy muffin recipes that are perfect for breakfast, snacks, and even dessert! From classic morning glory and lemon poppyseed muffins to rich chocolate muffins, and even savory cornbread muffins, these easy muffin recipes are easy to make, nourishing, and perfect for the whole family.

It's no secret that I have a real muffin obsession. The proof is in all these fabulous recipes I've perfected over the years! Vegan muffins, gluten free muffins, flourless muffins, low sugar muffins...there's something for everyone.
I love the versatility of muffins (you can eat them any time of day!), that they keep me full and satisfied for hours, and that you can't beat the smell of baking muffins in your kitchen!
How to store muffins
Store homemade muffins in a tightly covered (or airtight) container at room temperature for up to three days, or in the refrigerator for up to five days.
Want to freeze? Simple freeze the cooled muffins on a lined baking sheet or plate. Once frozen, place them into a freezer bag and they'll stay fresh for up to three months.
When you're ready to eat, thaw them on the countertop, or warm them in the microwave individually!
Are homemade muffins good for you?
As a nutrition professional, my recipes have much less sugar and fat when compared to store-bought, bakery, or other traditional muffins. My recipes often include whole grains, nuts and seeds, fiber, and fruits or vegetables, all while limiting processed sugars.
I love to use healthy oils like avocado oil and coconut oil, plus unrefined sweeteners like maple syrup, honey or coconut sugar.
Many of the recipes in this round-up are also egg or dairy-free, gluten-free, or vegan! You can feel good about sharing these recipes with toddlers and kids because they're made with wholesome ingredients.
What flour is best for muffins?
It really depends on the recipe, but I like to use whole wheat flour (for the fiber!), whole wheat pastry flour (so fluffy!), or a combo of almond and oat flour for gluten free muffins.
You could also use half whole wheat flour and half all-purpose flour, or even 100% all-purpose flour if that's what you have on hand! Just check the "ingredients" and "substitutions" section of each recipe for more details on what flour will work best.
Helpful muffin tools
- I love this muffin tin. Nothing sticks, so clean-up is a breeze.
- This muffin pan comes with a lid if you need to transport your muffins.
- A handy muffin scoop for easy and perfect muffin portioning.
- Silicone liners or paper liners for easy clean up.
Healthy muffin recipes
Fluffy Healthy Lemon Blueberry Muffins (Vegan!)
Fluffy Healthy Lemon Blueberry Muffins bursting with fresh lemon and juicy blueberries! Made with nourishing ingredients like whole grain flour, these moist muffins have half the sugar of classic muffins.
Healthy Chocolate Muffins
The best tall and fluffy Healthy Chocolate Muffins made with whole grains and naturally sweetened! Moist and not overly sweet to conquer chocolate cravings, plus 5g of protein per muffin. These taste like classic chocolate cupcakes!
Healthy Morning Glory Muffins
Made with almond and oat flour and packed with fresh orange juice, banana, and carrots, these super moist Healthy Morning Glory Muffins are an amazing snack or breakfast! Vegan and gluten-free.
Healthy Zucchini Muffins
Amazing moist and fluffy Healthy Zucchini Muffins! Whole grain and sweetened with coconut sugar. Freezer friendly plus easily made vegan! These are fab topped with my Cream Cheese Frosting.
Fluffy Vegan Blueberry Banana Muffins
Oh so fluffy, tender, and moist Vegan Blueberry Banana Muffins full of whole grains. These delicious muffins make the ultimate healthy snack or simple on-the-go breakfast! What a day to be alive! It's like my beloved Vegan Banana Bread had a baby. Or a cousin? I had so many of you asking if that luscious
Fluffy Vegan Pumpkin Muffins
Super moist and fluffy Vegan Pumpkin Muffins packed with an entire can of pumpkin! Perfectly sweet and terrific with coffee.
Fluffy Healthy Lemon Poppyseed Muffins (with Lemon Glaze!)
Fluffy, perfectly sweet Healthy Lemon Poppyseed Muffins bursting with fresh, bright lemon flavor! Made with nourishing ingredients like whole wheat flour, honey, and lemon zest. These freeze great and are a huge hit with kids.
Super Moist Flourless Zucchini Muffins (Gluten Free!)
Easy one-bowl Gluten Free Zucchini Muffins! These healthy, super moist flourless muffins make a delish breakfast, snack or dessert. Low in sugar and almost 6g of protein per muffin!
Nourishing Banana Coconut Muffins
Amazingly moist Banana Coconut Muffins made with wholesome ingredients like ripe banana, almond flour, oat flour, maple syrup, and plenty of toasty coconut! They make a delicious gluten free, dairy free snack or breakfast on the go.
Super Moist Gluten Free Banana Muffins (1 bowl!)
Super moist and tasty Gluten Free Banana Muffins with walnuts made in 1 bowl! Lightly sweetened with maple syrup, these muffins are the ultimate easy snack.
Flourless Gluten Free Apple Cinnamon Muffins
Easy 8-ingredient Gluten Free Apple Muffins made with no oil or refined sugar. Moist, fluffy and flourless with 6g of protein per muffin.
Nourishing Fluffy Orange Muffins
Tall and fluffy Orange Muffins bursting with citrus flavor from fresh orange juice and zest. Made with whole grain flour and yogurt for a super delicious and healthier spin on morning muffins!
Healthy Sweet Potato Muffins (1 bowl, no added sugar!)
Incredible Healthy Sweet Potato Muffins with no added sugar made in 1 bowl! Fluffy, moist, and irresistible. Gluten free and toddler approved!
Applesauce Oatmeal Muffins
Easy Applesauce Oatmeal Muffins are a tasty, healthy on-the-go breakfast! Made with oats, applesauce, peanut butter, maple syrup, and cinnamon. Make a batch for busy mornings!
Healthy Chocolate Banana Muffins (no added sugar!)
Healthy Chocolate Banana Muffins sweetened with dates and bananas for a tasty, satisfying snack with no added sugar! Free of eggs, dairy, and gluten.
Healthy Chocolate Zucchini Muffins
Super moist 100% whole grain Healthy Chocolate Zucchini Muffins with no oil and packed with veggies! Whip up a batch for easy healthy breakfasts on the go.
Fluffy Banana Chickpea Muffins (kid-friendly!)
Fluffy Banana Chickpea Muffins that are super moist, flourless and protein-packed! A fun kid-friendly healthy snack that's low in sugar and gluten free.
Fluffy Honey Cornbread Muffins
The most Amazing Cornbread Muffins with cheddar cheese--moist, fluffy and irresistible with a pat of butter, a drizzle of honey, with white bean chili, or in stuffing!
Flourless Gluten Free Pumpkin Muffins
Easy 7-ingredient Flourless Gluten Free Pumpkin Muffins made with no oil or refined sugar and packed with 6g of protein per muffin! So moist and fluffy.
Healthy Muffin Recipes: Healthy Chocolate Muffins
- Prep Time: 10 minutes
- Cook Time: 16 minutes
- Total Time: 26 minutes
- Yield: 10 muffins 1x
- Category: Desserts
- Method: Oven
- Cuisine: American
- Diet: Vegetarian
Description
The best tall and fluffy Healthy Chocolate Muffins made with whole grains and naturally sweetened! Moist and not overly sweet to conquer chocolate cravings, plus 5g of protein per muffin. These taste like classic chocolate cupcakes!
Ingredients
- 1 cup whole wheat flour*
- ½ cup almond flour
- ⅓ cup unsweetened cocoa powder (or cacao powder)
- 1 tsp baking powder
- 1 tsp baking soda
- ½ tsp fine sea salt
- ½ cup milk of choice (oat, cow's, almond, etc)
- ½ cup pure maple syrup
- 2 large eggs
- ¼ cup avocado oil (or melted and cooled coconut oil)
- 1 ½ tsp vanilla extract
- ½ cup chocolate chips, plus more for topping
Instructions
- Preheat the oven to 425 degrees Fahrenheit and grease a muffin tin with cooking spray.
- In a large mixing bowl, stir together whole wheat flour, almond flour, cocoa powder, baking soda, baking powder, and salt.
- In a medium bowl or liquid measuring cup, whisk together milk, maple syrup, oil, eggs, and vanilla.
- Pour the wet ingredients into the dry ingredients, stirring with a wooden spoon just until combined. Gently fold in ½ cup chocolate chips.
- Spoon batter evenly into 10 muffin cups. Top with additional chocolate chips if you like! Bake for 8 minutes at 425°F and then reduce the heat to 350°F (keeping muffins in oven) and bake for another 9-10 minutes, or until a toothpick comes out clean. Cool muffins in tin for 10 minutes before transferring to a wire rack to cool.
Notes
*All purpose flour, white whole wheat flour, or whole wheat pastry flour can be substituted for the whole wheat pastry flour. There are no substitutions for the almond flour as it contributes necessary fat for the recipe!
For sweeter muffins, you can increase maple syrup to ¾ cup.
Keywords: healthy chocolate muffins
Janelle says
I love all these recipes! The chocolate, morning glory, and GF banana are in regular rotation around here 🙂
★★★★★