Think muffins are always high in calories? Think again. These delicious low-calorie muffins are healthy enough that you might even enjoy two.
Sweet or savory, a flavorful healthy muffin with your morning coffee is one of the best ways to start the day.
Here are 20 low-calorie, healthy muffin recipes that will make store-bought muffins a thing of the past.
From fruit-packed and vegetable-forward to protein-rich and chocolatey, there’s a muffin here for every taste and occasion.
1. Egg Muffin Cups
Perfect for busy mornings, egg muffin cups are packed with vegetables and savory flavor. Broccoli, spinach, and peppers add crunch and color, making these a satisfying, portable breakfast option.
Per Serving:
- Calories: 81
- Fats: 3.7g
- Protein: 6g
- Carbs: 6.1g
- Fiber: 1.6g
- Sugar: 2.9g
2. Sweet Potato Muffins
These soft, nutty muffins combine sweet potato, applesauce, vanilla, and peanut butter with warm spices. Moist and nutrient-dense, they make a cozy afternoon snack everyone will enjoy.
Per Serving:
- Calories: 72
- Fats: 5g
- Protein: 3g
- Carbs: 5g
- Fiber: 1g
- Sugar: 2g
3. Keto Pepperoni Zucchini Muffins
These pizza-style zucchini muffins are well-seasoned and cheesy — ideal for breakfast, lunch boxes, or an on-the-go snack. They’re filling, full of flavor, and rich in protein.
Per Serving:
- Calories: 101
- Fats: 6.3g
- Protein: 6.2g
- Carbs: 5.2g
- Fiber: 1g
- Sugar: 2.2g
4. Carrot Cake Muffins
Quick and easy—this recipe uses boxed cake mix, water, and Greek yogurt for moist, simple carrot cake muffins. Add a handful of chocolate chips if you want a sweeter, more indulgent bite.
Per Serving:
- Calories: 23
- Fats: 1g
- Protein: 1g
- Carbs: 2g
- Fiber: 0g
- Sugar: 2g
5. Banana Bread Protein Muffins
Greek yogurt keeps these protein-packed banana muffins moist and tender. Stir in chopped nuts for extra fiber and a satisfying crunch.
Per Serving:
- Calories: 63
- Fats: 0.3g
- Protein: 6.2g
- Carbs: 9.6g
- Fiber: 1.1g
- Sugar: 1.5g
6. Banana Muffins
Made in an air fryer, these cinnamon-scented banana muffins are light, healthy, and easy to prepare. Mash bananas smooth for a uniform texture or leave some chunks for more bite. Top with chocolate for an extra treat.
Per Serving:
- Calories: 88
- Fats: 2.2g
- Protein: 2.3g
- Carbs: 15.9g
- Fiber: 1.9g
- Sugar: (varies)
7. Vegan Blueberry Muffins
Oats, dates, applesauce, soy milk, and flax combine with blueberries and cinnamon to create naturally sweet vegan muffins. Dates are key for natural sweetness, so don’t skip them.
Per Serving:
- Calories: 92
- Fats: 1g
- Protein: 3g
- Carbs: 19g
- Fiber: 3g
- Sugar: 8g
8. Quinoa Egg Muffins
Spinach, feta, and sun-dried tomatoes blend with quinoa and eggs for Mediterranean-style muffins that are filling and freezer-friendly—great for meal prep and quick lunches.
Per Serving:
- Calories: 97
- Fats: 5g
- Protein: 6g
- Carbs: 7g
- Fiber: 2g
- Sugar: 2g
9. Whole Wheat Strawberry Banana Protein Muffins
These fluffy banana and strawberry muffins are moist and satisfying, with optional chocolate chips for a dessert-like bite that still offers protein and fiber.
Per Serving:
- Calories: 104
- Fats: 2g
- Protein: 7g
- Carbs: 16g
- Fiber: 3g
- Sugar: 4g
10. Pistachio Muffins
Surprisingly light at about 23 calories per serving, these pistachio muffins are sweet, soft, and crunchy. The recipe calls for buttermilk, which you can easily make by adding lemon juice or vinegar to milk.
Per Serving:
- Calories: 23
- Fats: 0g
- Protein: 1g
- Carbs: 6g
- Fiber: (varies)
- Sugar: (varies)
11. Healthy Banana Muffins
Made with applesauce, spelt flour, and maple syrup—no refined sugar—these banana muffins are naturally sweet and nutrient-rich, perfect for kids and adults alike.
Per Serving:
- Calories: 107
- Fats: 1g
- Protein: 3g
- Carbs: 24g
- Fiber: 2g
- Sugar: 10g
12. Blueberry Muffin in a Mug
Ready in five minutes in the microwave, this single-serving blueberry muffin is quick, healthy, and sugar-free when prepared accordingly. Greek yogurt helps keep it moist.
Per Serving:
- Calories: 103
- Fats: 1g
- Protein: 6g
- Carbs: 18g
- Fiber: (varies)
- Sugar: (varies)
13. Keto Pumpkin Muffins
Light and airy, these low-carb pumpkin muffins use pumpkin puree and coconut flour for a moist, fragrant treat. Pumpkin pie spice and ginger amp up the autumnal flavor without added sugar.
Per Serving:
- Calories: 44
- Fats: 3.5g
- Protein: 4g
- Carbs: 3g
- Fiber: 2g
- Sugar: 1g
14. Carnitas Breakfast Muffins
These savory breakfast muffins deliver bold carnitas flavor with minimal carbs. Filling and protein-rich, they’re a hearty morning option—especially loved for their cheesy finish.
Per Serving:
- Calories: 71
- Fats: 2.4g
- Protein: 9.6g
- Carbs: 2.2g
- Fiber: 0g
- Sugar: 0g
15. Low Carb Pizza Muffins
These pizza-inspired bites combine pineapple and pickled jalapeño for a sweet-spicy kick. With a batch that yields many pieces, they’re great for parties or game nights.
Per Serving:
- Calories: 47
- Fats: 1.8g
- Protein: 4g
- Carbs: 3.5g
- Fiber: 0g
- Sugar: 0g
16. Chocolate Chip Muffins
Oats and applesauce replace heavier ingredients in these chocolate chip muffins, delivering classic indulgent flavor without empty calories. Cinnamon adds warmth and depth.
Per Serving:
- Calories: 94
- Fats: 3g
- Protein: 2g
- Carbs: 15g
- Fiber: 2g
- Sugar: 9g
17. Egg White Muffin Bites
Egg white muffin bites are a light, protein-packed breakfast. Customize with colorful vegetables and herbs for extra nutrients and flavor.
Per Serving:
- Calories: 100
- Fats: 3g
- Protein: 7g
- Carbs: 11g
- Fiber: 0g
- Sugar: 0g
18. Clean Eating English Muffins
These lighter English muffins clock in under 100 calories and have a soft texture that works well with jam, eggs, or spreads. They’re a lovely, filling alternative to traditional options.
Per Serving:
- Calories: 94
- Fats: 1g
- Protein: 3g
- Carbs: 16g
- Fiber: 2g
- Sugar: 1g
19. Healthy Egg Muffins
Turkey bacon-wrapped egg muffins filled with vegetables are a savory, protein-rich breakfast. Omit jalapeño if you prefer less heat; swap in your favorite veggies for variety.
Per Serving:
- Calories: 88
- Fats: 4.3g
- Protein: 10.8g
- Carbs: 2.1g
- Fiber: 0.6g
- Sugar: 1.3g
20. Breakfast Casserole Muffins
Crescent roll, diced ham, grated cheese, and egg come together in a casserole-style muffin that’s crispy, cheesy, and just about 100 calories each. These are great for a quick, energizing breakfast on the go.
Per Serving:
- Calories: 105
- Fats: 7g
- Protein: 5g
- Carbs: 9g
- Fiber: (varies)
- Sugar: 2g