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Whole Wheat Lemon Muffins

Whole Wheat Lemon Muffins are bright and cheery muffins made with white whole wheat flour, yogurt, coconut oil, and reduced sugar! They are perfect for an on-the-go breakfast or snack.

Whole Wheat Lemon Muffins

I absolutely adore lemon baked goods and its safe to say I don’t have enough of them on here. The handful that I do have, like these Creamy Creamy Lemon Crumble Bars, Lemon Blueberry Bundt Cake, Lemon Layer Cake with Raspberry Filling, and Lemon Almond Pound Cake are pretty stellar, though!

This time, I wanted to create a healthier lemon baked good and these Whole Wheat Lemon Muffins are what I came up with!

Healthy Lemon Muffins

Ingredients in Whole Wheat Lemon Muffins

White Whole Wheat Flour – I love using this whole grain flour because it keeps things light and not too heavy, as whole wheat flour sometimes does.

Sugar – I used a lower amount of sugar in these muffins than a typical muffin recipe, which keeps them sweet but not too sweet!

Lemon Zest and Juice – for maximum lemon flavor!

Plain Yogurt – a great way to keep things tender, without adding a ton of calories.

Coconut Oil – this adds a hint of coconut flavor to these muffins, which I love with the lemon!

Vanilla Extract – always so good!

Of course there are the other ingredients like baking powder, baking soda, milk, egg, and salt, too.

Healthy Lemon Muffins with whole wheat flour, coconut oil, Greek yogurt, and milk.

These lemon muffins are also finished off with a glaze that is made with powdered sugar, lemon juice, and milk. This is totally optional if you want to keep them on the healthier side, and they are absolutely delicious with or without the glaze. I made this batch half with and half without the glaze.

Substitutions for Lemon Muffins

Orange Zest and Juice – you can make these orange muffins if you’d like, by just using orange zest and just instead of lemon zest and juice.

Butter or Canola Oil – instead of melted coconut oil you can use melted butter or canola oil instead. Really any neutral oil would work!

All-Purpose Flour – you can definitely use all-purpose flour instead of white whole wheat flour. I wouldn’t use all whole wheat flour, though, as they won’t turn out quite as tender as this recipe.

These whole wheat lemon muffins were the perfect “first breakfast” for the boys and I. We have been waking up especially hungry lately and having a little snack before making actual breakfast. All of the muffins I’ve been making have been perfect for this!

Like this recipe? Check these out, too:

Lemon Zucchini Muffins

Lemon Poppy Seed Muffins

Whole Wheat Orange Blueberry Muffins from Super Healthy Kids

Whole Wheat Lemon Muffins

Whole Wheat Lemon Muffins

A healthier lemon muffin recipe made with white whole wheat flour and reduced sugar!
Print Pin Rate
Course: Breakfast
Cuisine: American
Keyword: muffin, lemon, white whole wheat flour, coconut oil, breakfast, snack, healthy
Prep Time: 15 minutes
Cook Time: 15 minutes
Total Time: 30 minutes
Servings: 12 muffins
Calories: 213kcal


  • 1/2 cup granulated sugar
  • 1 tbsp lemon zest from about 1 lemon
  • 1/2 cup plain yogurt
  • 1/2 cup milk I used unsweetened vanilla almond milk
  • 1/3 cup lemon juice from about 2 large lemons
  • 1 large egg at room temperature
  • 1 tsp pure vanilla extract
  • 1/3 cup coconut oil, melted
  • 2 cups white whole wheat flour
  • 1 tsp baking powder
  • 1 tsp baking soda
  • 1/2 tsp salt

For the Glaze:

  • 1 cup powdered sugar
  • 1 tbsp lemon juice
  • 1-2 tbsp milk


  • Preheat the oven to 350 degrees F.
  • Spray a 12 cup muffin pan with cooking spray.
  • In a large bowl, whisk together the sugar, lemon zest, yogurt, milk, lemon juice, vanilla extract, and egg.
  • Whisk in the coconut oil until well combined.
  • Add the flour, baking powder, baking soda, and salt, stirring in with a rubber spatula until combined.
  • Evenly divide the batter between the 12 muffin cups.
  • Bake in the preheated oven for 15-17 minutes, until the tops spring back
  • Once the muffins are cool, make the glaze.
  • In a small bowl, whisk together the powdered sugar, lemon juice, and milk.
  • Drizzle over the muffins.
  • Enjoy!


Calories: 213kcal | Carbohydrates: 34g | Protein: 4g | Fat: 8g | Saturated Fat: 6g | Cholesterol: 20mg | Sodium: 205mg | Potassium: 98mg | Fiber: 2g | Sugar: 19g | Vitamin A: 52IU | Vitamin C: 4mg | Calcium: 56mg | Iron: 1mg
Tried this recipe?Mention @greensnchocolate to let me know!
Need more ideas?Find all of my recipe pins @greenschocolate

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