If you’re craving a wholesome, bakery-style muffin that’s  packed with the good stuff, these Healthy Bran Muffins (filled with juicy apples and sweet raisins!) are about to become your new morning staple. They deliver that cozy, old-school bran-muffin magic… but with a modern, nutrient-packed makeover that supports steady energy, good digestion, and happy taste buds.

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Muffins are delicious! They are large and studded with raisins and apples. Made them as the recipe indicated and they were a hit with the whole family!

Linda
(4.92 stars) 12 ratings
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There’s something about the aroma of freshly baked bran muffins that transports me straight back to NYU grad school. I used to grab those oversized muffins from a fantastic little campus spot — Waverly Coffee Shop, right on the outskirts of Washington Square Park in Greenwich Village. They were SO BIG, subtly sweet, and the kind of “healthy-ish” treat (emphasis firmly on the ish, haha) that made me feel virtuous with every bite. I loved their flavor and that unmistakable bran-forward, nutty scent.

Fast-forward to today, and I’ve reimagined my nostalgic favorite with a better-for-you twist — far less sugar, heart-healthy fats, extra fiber, and a sneaky boost of protein from Greek yogurt, whole grain flour, and flax meal (or chia). These muffins are tender and satisfying. They’re perfect for breakfast, snack time, or an easy grab-and-go munchie.

If you’re craving more healthier baked goods, I’ve got a ton! Try my Apple Pie Baked Oatmeal, Blueberry Banana Protein Pastries, Breakfast Coffee Cookies, and Banana Chocolate Chip Muffins—all simple and scrumptious, and terrific for meal prep.

Reasons this recipe is a no-bran-er!

  • Full of fiber & energizing: Wheat bran, whole grains, and fruit provide fiber to support digestion and steady your stamina.
  • Soft, tender, and bakery-style comfort: Greek yogurt and applesauce give these muffins a moist, café-style texture.
  • Balanced nutrition in every bite: Some protein, some healthy fat, some natural sweetness… everything working together for a feel-good treat. 
  • Meal-Prep Friendly: They freeze wonderfully, reheat quickly, and hold up beautifully in lunchboxes or tote bags.

I love adding raisins and chopped apples for pizzazz, but they’re also wonderful with fresh blueberries—and even a sprinkle of dark chocolate chips. Truly no wrong turn… they’re delicious every which way!

A stack of Healthy Bran Muffins with Apples and Raisins (High-Protein & High-Fiber) sits on crinkled parchment paper, surrounded by a textured beige cloth, apples, and a small white bowl of raisins.

Make my Chocolate Energy Muffins next!

(4.92 stars) 12 ratings

Healthy Bran Muffins with Apples and Raisins (High-Protein & High-Fiber)

Wholesome, soft bran muffins loaded with apples and raisins. They’re gently sweet, high in fiber and protein, and incredibly satisfying—an easy, nourishing bake you’ll love warm from the oven or straight from the freezer stash.
Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
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Ingredients
 

  • 1 ½ cups white whole wheat flour, you can swap in all-purpose or a 1:1 gluten-free baking flour
  • 1 cup wheat bran
  • ¼ cup ground flaxseed or ¼ cup whole chia seeds
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon fine salt
  • ½ teaspoon ground cinnamon
  • 2 large eggs, at room temperature
  • 2 cups nonfat plain Greek yogurt
  • ½ cup pure maple syrup or honey
  • 2 to 3 tablespoons avocado oil, or other vegetable oil
  • ⅓ cup applesauce
  • 1 teaspoon vanilla extract
  • ⅔ cup raisins
  • 1 medium apple, finely chopped (skin-on, ~1 cup)

Instructions
 

  • Prep. Preheat your oven to 425°F. Liberally mist a standard 12-cup muffin tin with nonstick spray.
  • Mix the dry ingredients. In a large mixing bowl, whisk together the flour, wheat bran, ground flaxseed or chia, baking powder, baking soda, salt, and cinnamon.
  • Mix the wet ingredients. In a separate medium bowl, whisk the eggs with the Greek yogurt, maple syrup (or honey), avocado oil, applesauce, and vanilla until smooth and fully combined.
  • Bring it all together. Pour the dry mixture into the wet (this helps ensure none of the wet ingredients get stuck at the bottom of the bowl). Stir gently until just combined — avoid overmixing so your muffins stay tender. The batter will be very thick and spongy — this is normal. Fold in raisins, chopped apples, or any other add-ins you’d like. (Save a few to garnish the tops—or use extra!)
  • Fill muffin cups and bake. Divide the batter evenly among the 12 muffin cups (a lightly misted ½-cup measuring cup works well for portioning—use a scant ½ cup scoop). The compartments will be very full, with mounded tops. Add a few extra raisins and apple pieces on top for décor if you’d like. Bake for 5 minutes at 425°F, then — without opening the oven door! — reduce the temperature to 350°F and bake for an additional 15–16 minutes, or until a toothpick comes out clean. Total bake time: about 20 to 21 minutes.
  • Let muffins rest in the pan for 15 minutes, then carefully loosen the edges with a knife to remove them without breaking… and dig in! See notes below for storage.

Notes

Storage: Store covered at room temperature for 2–3 days, or refrigerate in a sealed container for up to 1 week. You can also wrap individually and freeze for up to 3 months. Thaw overnight or warm in the microwave for ~30 seconds.
Add-in inspiration: Try chopped dates, fresh blueberries, dried cherries, or dark chocolate chips!
Gluten-free option: Use a 1:1 gluten-free baking flour and a certified gluten-free bran alternative (such as oat bran).
Vegan option: Replace the eggs with flax eggs (mix 2 Tbsp ground flax + 6 Tbsp warm water and let it sit for 15 minutes, then add to the wet batter), use maple syrup instead of honey, and swap the Greek yogurt for a thick plant-based yogurt.
Author: Joy Bauer, MS, RDN, CDN

Nutrition Information per serving

Serving Size: 1 muffinCalories: 170Carbohydrates: 30gProtein: 8gTotal Fat: 3.5g— Unsaturated Fat: 3.5g— Saturated Fat: 0gCholesterol: 30mgSodium: 140mgPotassium: 236mgFiber: 4gTotal Sugar: 14g— Natural Sugar: 7g— Added Sugar: 7gIron: 1.6mg
Nutrition information is calculated using a leading industry software. That being said, brands can vary, and there may be slight fluctuations in the numbers.
I’m hoping you loved this recipe! If you made it and want to share feedback, I’d be so grateful to hear from you. Please leave a review below or tag @joybauer on Instagram!