Healthy Lemon Chia Seed Muffins

These lemon chia seed muffins are an absolutely delicious treat that you can enjoy for a great breakfast, an afternoon snack, or even as a dessert. With white whole wheat flour, chia seeds, and lots of lemon flavor- they’re a light, flavorful and nutritious muffin that’s super simple to make.

Lemon chia seed muffins arranged on a wooden serving board with lemon slices and a yellow kitchen towel.

Why you’ll love this muffin recipe

If you’re a lemon fan, you’re going to love these flavor-packed muffins. They’re full of bright lemon flavor and lightly drizzled with a delicious, sweet glaze.

We’re using a few swaps with nutrition in mind, but you won’t be sacrificing any flavor.

These lemon muffins are made with healthy, wholesome ingredients like white whole wheat flour, chia seeds, honey, and Greek yogurt. They have fiber, protein, and essential vitamins and minerals that will help keep you full and satisfied for longer.

Chia seeds in particular are packed with health benefits. When it comes to nutrition, their tiny little powerhouses!

They’re also really simple to make! You don’t need to be an experienced baker to throw this recipe together.

Let’s get into what you need!

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Ingredients for lemon chia seed muffins laid out on a white countertop with labels.

Ingredients you’ll need

Dry Ingredients

White whole wheat flour: My favorite white whole wheat flavor is from King Arthur Flour. It’s perfect if you want a whole wheat flour, but you want to make sure your baked goods don’t come out too dense.

Chia seeds: Chia seeds add fiber, healthy fat and texture to these muffins.

Baking powder, baking soda and salt: Baking powder and baking soda are essential to make sure your muffins to be light and fluffy. The small amount of salt brings out the sweetness!

Powdered sugar: This one’s optional, but if you want to top your muffins with a really easy lemon glaze, you’ll need powdered sugar.

Wet Ingredients

Honey: You can use any sweetener that you want here. Maple syrup, regular granulated sugar or coconut sugar would all work great here. Personally, I love the deep flavor that honey brings to baked goods.

Fresh lemon juice and fresh lemon zest: This lemon zester is my favorite. And bonus, you can use a zester to “mince” garlic in recipes!

Avocado oil: I love using avocado oil because it’s full of heart-healthy monounsaturated fats, antioxidants, and it’s super neutral flavored. You could also use canola oil, melted refined coconut oil, or melted butter.

Eggs and Greek yogurt: Greek yogurt helps to add moisture, tanginess and a creamy texture to the batter. Plus, it adds some protein and calcium! Eggs help bind the muffins together, and add some protein and nutrients too.

Vanilla extract: Vanilla extract helps to round out the flavor of these muffins.

Milk: Use whatever milk you like here! Regular dairy milk or plant-based milks will both work.

How to make them

  1. Preheat your oven to 350 degrees F (180 degrees C). In a large bowl, mix together the dry ingredients: flour, chia seeds, baking powder, baking soda, and salt.
  2. In a separate bowl, whisk together the wet ingredients: honey, Greek yogurt, eggs, milk, avocado oil, vanilla, lemon zest, and lemon juice.
The first two steps of lemon chia seed muffins are shown here: a mixture of dry ingredients and then the mixture of wet ingredients.

3. Add the wet ingredients to the dry ingredients and mix until just combined. Be careful not to over mix.

4. Line a muffin tin with muffin liners or grease the muffin cups (or use a silicone muffin pan). Scoop the batter evenly into the muffin cups, filling each about ⅔ full.

Steps 3 and 4 of making lemon chia seed muffins: a bowl is showing the mixed batter, and then a muffin pan lined and filled with batter.

5. Bake the muffins for 15-18 minutes or until a toothpick inserted into the center of a muffin comes out clean. Allow the muffins to cool for a few minutes before removing them from the muffin tin and placing them on a cooling rack to cool completely.

6. To make the glaze, whisk together the powdered sugar, lemon juice, and milk until smooth in a small bowl. Once the muffins have cooled, drizzle the glaze over the top of each muffin.

Steps 5 and 6 of making lemon chia seed muffins shown here: the baked muffins in the muffin pan are the first picture, and a muffin topped with glaze is the second picture.

Serve and enjoy!

Recipe FAQ

How can I turn this into a balanced breakfast?

These lemon chia muffins are a great carb choice for your breakfast with 3g of fiber and 5g of protein each! Pair them with a good protein source, like scrambled eggs. Add some fresh berries on the side for even more filling fiber (blueberries and lemon are a great flavor combination!).

For a super quick breakfast that doesn’t require any prep, pair a muffin with a Greek yogurt and some fruit!

Is white whole wheat flour the same as regular whole wheat flour?

It has the same nutritional benefits, but it’s a little different! White whole wheat flour has a lighter color, milder flavor, and softer texture compared to regular whole wheat flour, so it’s great for recipes where you want a lighter texture, like muffins!

Can I use all-purpose flour if I don’t have white whole wheat?

You can! They’ll be lower in fiber, but they’ll still be delicious.

How should I store them?

You can store the muffins in an airtight container at room temperature for up to 3 days, or in the refrigerator for up to 1 week. You can also freeze the muffins for up to 2 months. To reheat, simply microwave for a few seconds or warm in the oven for a few minutes.

Can I omit the glaze?

Yes, of course! If you prefer to keep it lower in added sugar, feel free to omit the glaze. The muffins are absolutely delish all on their own!

Lemon chia seed muffins arranged on a wooden serving board with lemon slices and a yellow kitchen towel.

Variations

Use oranges instead of lemons! Instead of using lemon juice and lemon zest, you can use orange juice and orange zest to give the muffins a different citrus flavor. Substitute the lemon juice and zest with equal amounts of fresh orange juice and zest, and follow the recipe as usual.

Add nuts. If you want to add some crunch and texture, you can add nuts such as chopped walnuts, pecans, or almonds. Fold in a 1/2 cup of your preferred nuts into the batter after all the other ingredients are mixed in.

Swap flaxseed for chia: If you prefer using flaxseed over chia seeds, you can substitute 3 tbsp of ground flaxseed for the 3 tbsp of chia seeds in the recipe. Flaxseed is also high in fiber and omega-3 fatty acids, making it a equally nutritious sub for chia seeds.

Add blueberries: For an extra burst of flavor and antioxidants, you can add a 1/2 cup of blueberries to the muffin batter (I prefer wild blueberries!). Fold them in after all the other ingredients are mixed in.

To turn this recipe into mini muffins, use a mini muffin tin instead of a regular-sized one and reduce the baking time to around 10-12 minutes or until a toothpick inserted into the center of a muffin comes out clean.

Sub in sour cream instead of Greek yogurt. Just keep in mind that sour cream has a slightly different flavor and texture than Greek yogurt, so the muffins may taste slightly different and have a slightly different texture.

More Delicious Recipes You’ll Love For Breakfast:

Banana Blueberry Oatmeal Muffins

Chocolate Oat Milk Chia Pudding

A close up shot of lemon seed muffins arranged on a wooden serving board with sliced lemons.

Healthy Lemon Chia Seed Muffins

Light and lemony chia seed muffins made with white whole wheat flour, chia seeds and fresh lemons.
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Course: Breakfast, Dessert, Snack
Prep Time: 10 minutes
Servings: 12
Calories: 201kcal

Ingredients

  • 2 cups white whole wheat flour
  • 3 tbsp chia seeds
  • 1 tsp baking powder
  • 1/4 tsp baking soda
  • 1/4 tsp salt
  • 1/2 cup honey
  • 1/2 cup plain Greek yogurt
  • 2 large eggs
  • 1/2 cup milk
  • 1/3 cup avocado oil
  • 1 tsp vanilla
  • 1 tbsp lemon zest
  • 1/4 cup lemon juice

Glaze (Optional)

  • 1/2 cup powdered sugar
  • 1 tbsp lemon juice or to taste

Instructions

  • Preheat your oven to 350 degrees F (180 degrees C).
  • In a large bowl, mix together the flour, chia seeds, baking powder, baking soda, and salt.
  • In a separate bowl, whisk together the honey, Greek yogurt, eggs, milk, avocado oil, vanilla, lemon zest, and lemon juice.
  • Add the wet ingredients to the dry ingredients and mix until just combined. Be careful not to over mix.
  • Line a muffin tin with muffin liners or grease the muffin cups (or use a silicone muffin pan)
  • Scoop the batter evenly into the muffin cups, filling each about ⅔ full.
  • Bake the muffins for 15-18 minutes or until a toothpick inserted into the center of a muffin comes out clean.
  • Allow the muffins to cool for a few minutes before removing them from the muffin tin and placing them on a wire rack to cool completely.
  • To make the glaze, whisk together the powdered sugar, lemon juice, and milk until smooth in a small bowl.
  • Once the muffins have cooled, drizzle the glaze over the top of each muffin.
  • Serve and enjoy!

Notes

If you don’t have fresh lemons, you can sub in 2 tsp lemon extract.

Nutrition

Calories: 201kcal | Carbohydrates: 28g | Protein: 5g | Fat: 8g | Saturated Fat: 1g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 5g | Trans Fat: 0.01g | Cholesterol: 32mg | Sodium: 127mg | Potassium: 88mg | Fiber: 3g | Sugar: 13g | Vitamin A: 68IU | Vitamin C: 3mg | Calcium: 81mg | Iron: 1mg

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