Chocolate chip muffins are a timeless treat, but often come packed with sugar and unhealthy fats. The good news? You don’t have to sacrifice flavor for health. We’ve gathered 12 delicious and wholesome chocolate chip muffin recipes that incorporate nutritious ingredients like fruits, vegetables, whole grains, and healthy fats. Whether you’re looking for a quick breakfast, a satisfying snack, or a lighter dessert, these recipes offer a healthier twist on a beloved classic.

1. Greek Yogurt Chocolate Chip Muffins

Greek Yogurt Chocolate Chip Muffins

Using plain non-fat Greek yogurt creates a tender crumb while boosting the protein content in this lighter baked treat.

Get the Recipe

2. Healthy Banana Oat Chocolate Chip Muffins

Healthy Banana Oat Chocolate Chip Muffins

These hearty muffins use rolled oats and ripe bananas for natural sweetness, offering a fiber-rich start to the morning.

Get the Recipe

3. Flourless Peanut Butter Chocolate Chip Muffins

Flourless Peanut Butter Chocolate Chip Muffins

These gluten-free muffins rely on creamy natural peanut butter and honey to create a soft and moist texture without any flour.

Get the Recipe

4. Healthy Double Chocolate Muffins

Healthy Double Chocolate Muffins

Cocoa powder and dark chocolate chips combine with unsweetened applesauce for a rich flavor profile that is surprisingly low in added oil.

Get the Recipe

5. Spiced Pumpkin Chocolate Chip Muffins

Spiced Pumpkin Chocolate Chip Muffins

Pure pumpkin puree and warm autumn spices pair expertly with dark chocolate chips in this nutrient-dense recipe.

Get the Recipe

6. Whole Wheat Zucchini Chocolate Chip Muffins

Whole Wheat Zucchini Chocolate Chip Muffins

Shredded zucchini adds significant moisture to these 100% whole grain muffins without overpowering the classic chocolate flavor.

Get the Recipe

7. Raspberry Chocolate Chip Oatmeal Muffins

Raspberry Chocolate Chip Oatmeal Muffins

Tart fresh raspberries cut through the sweetness of the semi-sweet chocolate chips in this hearty oat-based muffin.

Get the Recipe

8. Fudgy Avocado Chocolate Chip Muffins

Fudgy Avocado Chocolate Chip Muffins

Ripe avocado provides healthy fats and a creamy texture, making these chocolate-packed muffins incredibly moist without butter.

Get the Recipe

9. Cinnamon Applesauce Chocolate Chip Muffins

Cinnamon Applesauce Chocolate Chip Muffins

Unsweetened applesauce replaces most of the fat in these fluffy muffins, highlighted by a generous dusting of cinnamon.

Get the Recipe

10. Almond Flour Chocolate Chip Muffins

Almond Flour Chocolate Chip Muffins

A grain-free option that uses ground almonds to create a nutty, dense, and satisfying baked good suitable for paleo diets.

Get the Recipe

11. Maple Walnut Chocolate Chip Muffins

Maple Walnut Chocolate Chip Muffins

Sweetened entirely with pure maple syrup, these whole wheat muffins feature crunchy walnuts for added texture and omega-3s.

Get the Recipe

12. Sweet Potato Chocolate Chip Muffins

Sweet Potato Chocolate Chip Muffins

Mashed sweet potato adds vitamins and a vibrant orange hue to these naturally sweetened snacks that kids love.

Get the Recipe