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The 10 Best Healthy Muffin Recipes, According to Nutritionists

Swap the traditional sugar-laden muffins for these nutritionist-approved healthy muffin recipes that use ingredients that are naturally sweet, like pumpkin, zucchini, carrots, and more.

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Easy healthy muffin recipes

As muffin lovers know: Muffins can be packed with hundreds of calories. Or they can be a healthy treat. The trick? Using less added sugar and utilizing more nutrient-packed, naturally sweet ingredients such as banana, pumpkin, and carrots.

Portion size is also key—as well as minimizing those crumbly, often butter-filled toppings.

To help you start your mornings on a healthier note, check out these 10 delicious, good-for-you muffin recipes—all, from registered dietitians.

orange juice cranberry muffinCourtesy Amy Gorin, MS, RDN

Orange Juice Muffins

Mouthwatering muffins made with orange juice, banana, and dried cranberries? Yes, please. These protein-offering muffins come from my own plant-based kitchen. I love incorporating them into a balanced flexitarian eating plan. They’re naturally pretty low in added sugar, which is an extra bonus.

Makes 18 muffins

Ingredients:

  • 1 cup all-purpose flour
  • 1 cup whole-wheat flour
  • ½ cup sugar
  • 1 tbsp. baking powder
  • ¼ tsp. kosher salt
  • ¾ cup 100-percent orange juice
  • 1 cup low-fat plain Greek yogurt
  • 2 eggs
  • 1 tsp. vanilla extract
  • 1 ½ bananas, ripe and mashed
  • 3 tbsp. orange zest (roughly the zest of one large orange)
  • 1 cup dried cranberries
  • Cooking spray

Instructions:

Preheat oven to 350 degrees F. In a large bowl, whisk together the all-purpose flour, whole-wheat flour, sugar, baking powder, and salt. In another bowl, whisk together orange juice, yogurt, eggs, vanilla, and banana. Add liquid mixture to dry mixture, and stir until just combined. Fold in orange zest and cranberries.

Coat muffin trays with cooking spray, and fill three-quarters of the way with batter. Bake 14-16 minutes, or until a toothpick inserted in the center comes away clean.

savory breakfast muffinsCourtesy Shannon A. Garcia, MDS, RD

Savory Breakfast Muffins

When it comes to healthy muffin recipes, savory may be unexpected—but it usually means lower in sugar. “These muffins are both sweet and savory—and are loaded with protein and fiber,” says Shannon A. Garcia, RD, a nutrition blogger with KISS in the Kitchen in San Antonio. “They’re lightly sweetened with maple syrup and are guaranteed to be a crowd pleaser.”

Makes 18 muffins

Ingredients:

  • Cooking spray
  • 2 cups gluten-free oat flour
  • 2 cups super-fine blanched almond flour
  • ½ tsp. salt
  • 1½ tsp. baking soda
  • 4 eggs, slightly beaten
  • ½ cup maple syrup
  • 1 cup unsweetened almond milk (or dairy-free milk of choice)
  • 2 tbsp. butter, melted
  • 2 tsp. apple cider vinegar (or fresh lemon juice)
  • 2½ cups sharp cheddar cheese, divided
  • 1 cup cooked and crumbled bacon

Instructions:

Preheat oven to 350 degrees F. Coat the inside of 18 muffin cups with avocado oil or cooking spray of choice. Whisk together the oat flour, almond flour, salt, and baking soda in a large bowl.

In a separate large bowl, mix together the eggs, maple syrup, almond milk, butter, and apple cider vinegar until well combined. Add the dry ingredients to the wet ingredients, and stir until just combined.

Fold in 1½ cups of cheese. Divide batter evenly among 18 muffin cups, filling three-fourths of the way full. Bake for 15-18 minutes, until inserted toothpick comes out clean or just crumbly. Remove from oven.

Top muffins with crumbled bacon and 1 cup cheese. Return muffins to oven, and cook for an additional 2-3 minutes, until the cheese is just melted. Remove muffins from oven and allow to cool for 10 minutes. Remove from pan and place on wire rack to cool completely.

blueberry oat muffinsCourtesy Marie Dittmer, MA, RDN

Blueberry Oat Muffins

Let’s face it: Blueberry muffins are a morning staple. But it would be nice if they were healthy, right? “Breakfast just got better with these mouthwatering, homemade blueberry oat muffins,” says Marie Dittmer, RDN, owner of Healthy Ideas Place. “Filled to the brim with fresh blueberries and whole grains, these muffins are nourishing and filling.”

Makes 18 muffins

Ingredients:

  • Cooking spray
  • 2 cups whole-wheat pastry flour
  • 1 cup old-fashioned oats
  • 2 tbsp. ground flaxseeds
  • 2/3 cup sugar
  • ½ tsp. salt
  • 1 tbsp. baking powder
  • 2 eggs
  • ½ cup vegetable oil
  • ½ cup Greek yogurt
  • ½ cup milk
  • ½ tbsp. vanilla extract
  • 1 tbsp. fresh lemon zest
  • 1½ cups fresh blueberries
  • 1 tbsp. turbinado sugar

Instructions:

Preheat oven to 400 degrees F. Coat the bottoms of muffin cups with cooking spray or line them with paper muffin cups. In a large bowl, mix together the flour, oats, flaxseeds, sugar, salt, and baking powder. In a separate, smaller bowl, whisk together the eggs, oil, yogurt, milk, vanilla, and lemon zest.

Make a small well in the center of the dry ingredients, and pour the egg mixture into the dry ingredients. Gently mix all the ingredients together just until the dry ingredients are evenly moistened. Fold blueberries into the batter. Do not over mix.

Fill muffin cups two-thirds to three-quarters full. Sprinkle tops of muffins with turbinado sugar. Place muffins in oven, and bake for about 15 minutes, or until muffins are golden brown. Remove from oven and immediately cool on wire rack.

vegan spinach muffinsCourtesy Erin Cooper, RD

Vegan Spinach Muffins

Spinach in a muffin? Yes, it’s a thing. “These fluffy and festive vegan muffins are made with whole wheat flour and sweetened with bananas and a touch of maple syrup,” says Erin Cooper, RD, nutrition blogger at Cashews & Quinoa in San Clemente, California. “Plus, they’re packed with a powerful punch of spinach!”

Makes 12 muffins

Ingredients:

  • Cooking spray
  • 1 “flax egg” (1 tbsp. flaxseed meal + 2½ tbsp. water)
  • ¾ cup almond milk
  • ½ cup coconut oil, melted
  • ⅓ cup maple syrup
  • 1 tsp. vanilla extract
  • 1 large, very ripe banana
  • 6 ounces baby spinach
  • 2 cups whole wheat flour
  • 1½ tsp. cinnamon
  • ½ tsp. baking soda
  • 2 tsp. baking powder
  • ¼ tsp. salt

Instructions:

Preheat the oven to 350 degrees F. Prepare a muffin tin with cooking spray or muffin liners. In the bowl of your blender, combine water and flaxseed meal. Stir to combine, and allow to sit for 10 minutes until jelled. Once the flax egg is set, add almond milk, coconut oil, maple syrup, vanilla, banana, and spinach. Blend until well combined and spinach is incorporated.

Add flour, cinnamon, baking soda, baking powder, and salt. Blend until just combined, stopping periodically to scrape down the sides of the bowl. Fill each muffin tin three-quarters of the way to the top. Bake for 20-25 minutes, or until golden and toothpick inserted into the center comes out clean.

flourless banana oatmeal muffinsCourtesy Maggie Farley, MA RD

Flourless Banana Oatmeal Muffins

“This recipe is simple to follow, gluten-free, and all-natural,” says Maggie Farley, RD, owner of Meals with Maggie. “The muffins are made with a banana, peanut butter, honey, and oatmeal. Being full of fiber, healthy fats, and protein makes them a great option for a snack.”

Makes 12 muffins

Ingredients:

  • 1 cup rolled oats
  • 1 tsp. baking soda
  • 1 tsp. baking powder
  • ½ tsp. cinnamon
  • ¼ tsp. nutmeg
  • ¼ tsp. salt
  • 1 large overly ripened banana (or 2 small bananas)
  • 2 eggs
  • ½ cup creamy peanut butter
  • 3 tbsp. milk (or dairy-free milk, such as unsweetened vanilla almond milk)
  • ¼ cup honey
  • 1 tsp. vanilla extract
  • ½ cup chocolate chips

Instructions:

Preheat oven to 350 degrees F, and prepare muffin tin with liners. Pour oats into a food processor or blender until oats break down. In a large bowl, combine all dry ingredients and mix until combined. In another bowl, mash banana until smooth. Whisk in eggs, and add peanut butter, milk, honey, and vanilla.

Pour wet ingredients into dry ingredients, and mix. Once combined, add in chocolate chips. Fill muffin cups about halfway full. If you have batter left over, evenly pour the remaining into muffin cups. Bake for about 15-18 minutes, or until toothpick comes out clear.

zucchini muffinsCourtesy Ginger Hultin, RD

Healthy Anytime Zucchini Muffins

Here’s another delicious way to eat your veggies in a baked good. “These zucchini muffins are flavorful, moist, and even include a veggie for more fiber and texture—plus added vitamins and minerals like potassium and vitamin A,” says Ginger Hultin, RD, owner of Champagne Nutrition in Seattle.

Makes 12 muffins

Ingredients:

  • ¾ cup whole wheat flour
  • 1 cup all-purpose flour
  • ½ cup rolled oats
  • 1 tsp. baking powder
  • 1 tsp. baking soda
  • 1 tsp. cinnamon
  • 1 tsp. salt
  • 2 eggs
  • ½ cup maple syrup
  • ½ cup soy milk (or dairy, oat, or almond milk)
  • ½ cup vegetable oil (such as grapeseed, canola, or avocado)
  • 1 tsp. vanilla extract
  • 2 small zucchinis, grated and pressed gently with paper towels to remove moisture

Instructions:

Heat oven to 375 degrees F, and line a 12-cup muffin tin with paper or silicone liners. Alternatively, grease the muffin tins. In a large mixing bowl, whisk together whole wheat flour, all-purpose flour, oats, baking powder, baking soda, cinnamon, and salt. In a separate medium mixing bowl, whisk together eggs, maple syrup, milk, oil, and vanilla.

Pour the wet mixture into the dry mixture, and stir with a wooden spoon to combine. Gently fold in the zucchini, until just incorporated. Divide the batter evenly among the muffin tins and bake for 18-20 minutes, or until muffin tops are firm to the touch.

spiced carrot raisin muffinsCourtesy Melissa Altman-Traub MS, RDN, LDN

Spiced Carrot Raisin Muffins

These muffins—with both carrots and raisins—are full of plant-based nutrients. “Here are some tasty fall muffins filled with fall flavors,” says Melissa Altman-Traub, RDN, a dietitian in Bucks County, Pennsylvania. “They are high in fiber and reduced in sugar and fat.”

Makes 12 muffins

Ingredients:

  • ½ cup raisins
  • 6 ounces vanilla soy milk
  • 1 tbsp. apple cider vinegar
  • Cooking spray
  • 1 cup whole wheat flour
  • 1 cup all-purpose flour, unbleached
  • ⅓ cup brown sugar
  • 1 tsp. baking powder
  • 1 tsp. cinnamon
  • 1 tsp. baking soda
  • ½ tsp. salt
  • ½ tsp. ginger, powdered
  • ¼ tsp. allspice
  • 1 cup grated carrots
  • 4 ounces natural applesauce
  • ⅓ cup olive oil
  • 2 ounces water

Instructions:

Soak the raisins in warm water. Mix soy milk with vinegar, and stir. Set aside.

Preheat oven to 400 degrees F. Coat 12 muffin cups with cooking spray, or place a cupcake wrapper in each. In a large bowl, whisk together the dry ingredients.

Drain the raisins and combine with grated carrots, then add to the bowl of dry ingredients, using a wooden spoon. In a small bowl, whisk together the soy milk-vinegar, applesauce, olive oil, and water. Add to the large bowl. Mix all ingredients together until just combined.

Place a half cup of batter into each muffin cup. Bake for 16 minutes or until the tops are lightly browned. Cool for 5-10 minutes in the pan, until the muffins can be handled. Then remove from the pan and finish cool on a baking rack.

honey pear pistachio muffinsCourtesy Rachael Hartley, RD

Honey Pear Pistachio Muffins

“Made with a blend of two whole grain flours—whole wheat flour and quinoa flour—these muffins are packed with fiber, which is filling, keeps your digestion on point, and is heart-healthy,” says Rachael Hartley, RD, owner of Rachael Hartley Nutrition. Get more healthy breakfast ideas.

Makes 12 muffins

Ingredients:

  • Cooking spray
  • 1¼ cups quinoa flour
  • 1½ cups whole wheat flour
  • 1 tbsp. baking powder
  • ¼ tsp. salt
  • ½ tsp. cinnamon
  • 2 pinches nutmeg
  • 2 pinches cardamom
  • 1½ cups milk (or almond milk)
  • ½ cup extra-virgin olive oil
  • 1/3 cup honey
  • 1 large egg
  • 1 tsp. vanilla extract
  • 2 pears, divided
  • ½ cup shelled pistachios

Instructions:

Preheat oven to 350 degrees F. Grease or butter a 12-cup muffin tin. In a large bowl, whisk together quinoa flour, whole wheat flour, baking powder, salt, cinnamon, nutmeg, and cardamom. In a medium bowl, whisk together milk, oil, honey, egg, and vanilla. Whisk wet ingredients into dry until fully incorporated.

Using the large holes of a cheese grater, grate 1½ pears. Fold grated pear into the batter along with the pistachios.

Divide batter evenly among the wells of the muffin tin. Cut thin slices of pear from the remaining pear half and top the muffins. Place in the oven and bake for 22-25 minutes until set and a toothpick inserted into the middle comes out clean.

sweet potato chai muffinsvia sarahpflugradt.com

Sweet Potato Chai Muffins

Healthy muffin recipes also entail fruits and veggies. “I’m a huge fan of adding fruits and veggies to muffins,” says Sarah Pflugradt, RDN, owner of Sarah Pflugradt Nutrition. “It increases the nutritional value and keeps them moist. These muffins also have less sugar than store-bought muffins and use ingredients you already have.”

Makes 12 muffins

Ingredients:

  • Cooking spray
  • 1 medium baked or roasted sweet potato flesh (about 1 cup mashed)
  • 1/3 cup canola oil
  • 1/2 cup 2% milk
  • 1 large egg
  • 1/3 cup granulated sugar
  • 1 tsp. vanilla extract
  • ¾ cup all-purpose flour
  • ¾ cup whole wheat flour
  • 2 tsp. baking powder
  • 1 tsp. cinnamon
  • 1 tsp. allspice
  • ½ tsp. nutmeg
  • ½ tsp. ground ginger
  • ½ tsp. table salt
  • ¼ tsp. cardamom
  • ¼ cup rolled oats

Instructions:

Preheat oven to 400 degrees F. Coat a 12-count muffin tin with cooking spray. In a medium mixing bowl, add sweet potato, oil, milk, egg, sugar, and vanilla. Mix until combined. In a small mixing bowl, add the remaining dry ingredients (except the oats); mix until combined.

Add dry ingredients to the wet ingredients, and stir until just combined. Fill each muffin cup with batter, about two-thirds of the way full. Sprinkle the oats on top of each one.

Bake for 20-22 minutes or until the muffins are lightly golden on top and a toothpick inserted into the center of the biggest muffin comes out clean.

whole wheat pumpkin muffinsCourtesy Vahista Ussery, MS, MBA, RDN

Whole-Wheat Pumpkin Muffins

‘Tis the season for pumpkin muffins. “These whole-wheat pumpkin muffins are packed with whole wheat flour and a whole can of pumpkin puree,” says Vahista Ussery, RDN, at To Taste. “They’re super easy to make, plus they’re great for storing in the freezer, making busy mornings a breeze.”

Makes 12 muffins

Ingredients:

  • Cooking spray
  • 1 cup whole wheat flour
  • ½ cup all-purpose flour
  • ½ tbsp. pumpkin pie spice
  • 1 tsp. baking soda
  • ¾ tsp. salt
  • ½ tsp. baking powder
  • 1 15-ounce can pure pumpkin
  • ¾ cup brown sugar
  • 2 large eggs
  • ¼ cup canola oil

Instructions:

Preheat oven to 350 degrees F. Prepare a 12-cup muffin pan with cooking spray or muffin liners. In a large bowl, gently whisk whole wheat flour, all-purpose flour, pumpkin pie spice, baking soda, salt, and baking powder. In a separate large bowl, whisk pumpkin, sugar, eggs, and oil until combined. Add pumpkin mixture to flour mixture.

Using a spatula, fold ingredients until just moistened. Do not over mix. Portion about ¼ cup batter into each cup. Bake 15-20 minutes or until slightly golden and a toothpick inserted into the middle comes out clean.

Sources

Amy Gorin, MS, RDN
Amy Gorin is a freelance writer and owner of Amy Gorin Nutrition in the New York City area. Connect with her on Facebook, Instagram, Twitter, and Pinterest.