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Healthy Lemon Blueberry Muffin Recipe

February 26, 2025 by Lily @ Nourish & Enjoy Leave a Comment

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These healthy blueberry muffins are buttery, fluffy and bursting with vibrant lemon blueberry flavor. Made with wholesome ingredients they are the perfect balance of nutritious and delicious.  

An image of freshly baked blueberry muffins cooling on a metal wire rack, placed on a wooden surface. The muffins have a golden-brown top with visible blueberries baked into them, giving them a delicious, speckled appearance. Scattered around the rack are a few fresh blueberries, a lemon, and some green leaves, adding a vibrant, appetizing touch to the scene. It looks like a cozy, homemade baking setup, perfect for enjoying a sweet treat!
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I have been making these incredible healthy lemon blueberry muffins for years. It’s become one of my kids favorite snacks. Usually we polish off the pan while they are still warm. They’re perfect for a breakfast treat, afternoon snack or even dessert. You will be lucky to have leftovers. 

This lemon blueberry muffin recipe only takes 30 mins, with only a few basic ingredients. I prefer to use freshly milled flour, but unbleached white whole wheat flour from the store works as well.  

What makes these lemon blueberry muffins healthy?

These muffins are made with freshly milled wheat grain. The fresh milled flour enhances the fresh flavor aroma! I compare it to a cup of coffee. Would you rather have a cup of coffee made with freshly ground beans or those ground months ago? 

Unlike all-purpose flour, freshly milled flour contains the bran, germ, and endosperm, all of which contain nutritional value. The bran is high in fiber, and contains protein. The germ is rich in fatty acids, vitamin E and minerals. The endosperm contains the starch. In contrast, all-purpose flour is stripped of the bran and germ, only providing the endosperm, which has very little nutritional content. 

The Star Ingredients: Lemon and Blueberries

I prefer to use fresh blueberries. I find them more vibrant, juicy, and bursting with fresh blueberry flavor. The lemon adds the perfect zing and bright aroma to the muffins. 

Naturally Sweetened with Honey

These lemon blueberry muffins are naturally sweetened with honey, my preferred sweetener. It has potential anti-inflammatory properties and immune boosting benefits.

Packed with Protein

The greek yogurt adds protein and an irresistible tang to these lemon blueberry muffins. I chose to make these muffins with butter for the rich buttery flavor and fat-soluble vitamins. These healthy lemon blueberry muffins have the perfect balance of protein, fat, and carbs!

Healthy lemon blueberry muffin tips: 

  • Measure flour properly: use a spoon-and-level technique to measure flour to avoid packing too much flour into the measuring cup. 
  • Frozen blueberries: do not defrost frozen blueberries before adding them to the batter. If thawed, they release extra moisture to the batter making it purple. 
  • Coat the blueberries: toss the blueberries with 1 tbsp of flour before adding them into the batter. This will prevent the blueberries from sinking to the bottom of the muffin. 
  • Do not overmix: fold the flour and blueberries into the batter gently to avoid dense muffins.

Optional Add-ins:

  • For an extra burst of lemon flavor and aroma, add in the zest of 2 lemons instead one just 1. 
  • Sprinkle 1/4 tsp of turbinado sugar on top of each muffin before baking for a golden sweet sparkle on each muffin top.

STORAGE TIPS

Leftover muffins can be stored at room temperature for up to 2 days or in the fridge for up to 1 week.

MORE RECIPES TO ENJOY:

  • Healthy granola recipe

If you make these healthy lemon blueberry muffin recipe, I’d love to hear how it turned out! Please share your thoughts in the comment section below.

An image of freshly baked blueberry muffins cooling on a metal wire rack, placed on a wooden surface. The muffins have a golden-brown top with visible blueberries baked into them, giving them a delicious, speckled appearance. Scattered around the rack are a few fresh blueberries, a lemon, and some green leaves, adding a vibrant, appetizing touch to the scene. It looks like a cozy, homemade baking setup, perfect for enjoying a sweet treat!
Print Recipe

The Best Healthy Lemon Blueberry Muffins

These healthy lemon blueberry muffins are buttery, fluffy, and bursting with flavor. They are high in protein, loaded with antioxidants, and perfectly sweetened. Make these for the perfect breakfast, afternoon snack, or dessert.
Prep Time10 minutes mins
Cook Time20 minutes mins
Total Time30 minutes mins
Course: Dessert
Cuisine: American
Keyword: bake, berries, blueberry, blueberry muffins, Healthy, high protien, Lemon, lemon blueberry muffins, lemon muffins, muffins, sugar free
Servings: 12 people
Calories: 30kcal
Cost: $5

Ingredients

Wet Ingredients

  • ⅓ cup Unsalted melted butter
  • ½ cup Honey
  • 2 Eggs
  • 1 cup Whole milk greek yogurt
  • 1 tsp Vanilla extract
  • 1 Zest of 1 lemon
  • 1/4 cup Lemon juice (about one lemon)

Dry Ingredients

  • 2 cups Freshly milled hard white wheat flour
  • 1 tbsp Freshly milled hard white wheat flour to coat blueberries
  • 1½ cups Blueberries fresh or frozen (don't thaw if frozen)
  • 1 tsp Baking soda
  • 1 tsp Baking powder
  • ½ tsp Salt
  • 1 tbsp Turbinado sugar (optional)

Instructions

  • Preheat oven to 400℉. Grease the muffin tin with butter or coconut oil (you can skip this if you're using a nonstick pan).
  • In a medium mixing bowl combine the melted butter, honey and eggs. Whisk well. Then add yogurt, vanilla, lemon juice and zest and whisk again. Mix until smooth and ingredients are well incorporated.
    image shows a collection of ingredients (blueberries, flour, yogurt, honey, butter, eggs, lemon, baking soda,salt) and measuring tools arranged on a wooden surface
  • In a large mixing bowl, whisk together the flour, baking soda, baking powder & salt.
  • Add the wet ingredients into the dry ingredients and mix with a spoon until well combined. Be careful not to over mix, as this can lead to dense muffins.
  • In a small bowl, toss the blueberries with 1 tablespoon of flour (this helps prevent them from sinking to the bottom while baking). Gently fold the blueberries into the muffin batter.
  • Divide the batter evenly among the 12 muffin cups.
  • Optional: sprinkle the top of each muffin with a pinch of turbinado sugar for a golden sparkle
  • Bake for 18-22 minutes or until the muffins are golden on top and a toothpick inserted into the center of the muffin comes out clean.
  • Allow the muffins to cool in the muffins tin for 5 minutes, then remove from pan and place on a wire cooling rack and allow to cool completely.
  • Leftover muffins can be stored at room temperature for up to 2 days or in the fridge for up to 1 week.

Notes

Recipe Notes:
Avocado oil or any other neutral oil may be substituted for the melted butter.  
Maple syrup may be substituted for the honey. 
For extra lemon flavor, add zest from 2 lemons instead of 1. 

Filed Under: Breakfast, Dessert, Recipes

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Hi, I’m Lily!

I’m a wife, crunchy mama of 3, NICU nurse and health enthusiast. I’m passionate about making nourishing food from scratch for my family to enjoy. Follow along for new healthy recipes for your family every single week! Read more about me here.

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