Lemon Chia Seed Muffins

Fluffy, tender Lemon Chia Seed Muffins are full of bright lemon flavor! They’re made in less than 30 minutes with healthy ingredients like avocado oil, fresh lemon and honey. Enjoy as a snack or quick breakfast!

If you’re looking for a healthier lemony treat, these lemon chia seed muffins are it. I updated the recipe in January 2026 to make it more nourishing, but they’re still soft, yummy, and full of bright lemon flavor.

I swapped the butter for avocado oil and was pleasantly surprised by how flavorful they still are. I also added an extra egg for more protein and used Greek yogurt and honey.

Chia seeds add crunch as well as fiber, antioxidants and omega-3 fatty acids. These muffins have that kind of healthy goodness I love in my chocolate muffins with avocado.

Love the original recipe? You’ll find it in the notes section of the recipe card below!

Why We Love This Recipe

• Bright & Lemony: Lemon zest and lemon juice pack fresh lemon flavor in every bite just like my lemon curd tart!
• Soft & Moist: Greek yogurt, avocado oil, and honey keep these muffins tender and moist without using butter. They have a texture similar to my lemon and ricotta muffins.
• Easy to Make: No mixer needed. The batter comes together in minutes with simple pantry ingredients.
• Wholesome & Flavorful: Chia seeds add great texture and a little extra goodness, while vanilla and lemon keep the flavor classic and cozy.

Ingredients

• I use all-purpose flour to keep this recipe pantry-friendly. You could also do half whole wheat and half all-purpose for added nutrition.
• They’re packed with a little extra protein thanks to Greek yogurt. I recommend plain whole milk. It’s the same ingredient I use in my olive oil grapefruit cake to make it tender and moist.
• These are naturally sweetened with honey.
• Chia seeds are a must for chia muffins!
• I use avocado oil for neutral flavor, but olive oil or melted coconut also works well.
• We’re using both fresh lemon juice and zest in the batter and in the optional icing. You’ll need about 2 large lemons. If you love bold lemon flavor, you’ll love my homemade lemon curd recipe and lemon and lime bars.
• For some added crunch and extra lemon flavor, top the muffins with some optional turbinado sugar and lemon zest before baking!

Substitutions

• Swap in vanilla and or 2% yogurt.
• For a more indulgent variation, use melted, slightly cooled unsalted butter.
• If you’d like to use granulated sugar, I recommend using 2/3 cup.
• I have not tested this recipe with maple syrup, but I think it would make a good substitute for the honey.

Instructions

Expert Tips

• Use organic lemons, if possible. Regular lemons are covered in a wax coating that can dilute the flavor in the zest. Organic lemons are free of this coating, and have a stronger lemon zest flavor.
• Mix the batter until just combined! This will give you light and tender muffins rather than muffins that are dense and tough.
• Grease your muffin pan with butter or non-stick spray or use cupcake liners so you can easily remove them once baked.
• If you’re eating one of these muffins after the day they were baked, warm them in the microwave for a few seconds for best flavor and texture.

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Lemon Chia Seed Muffins

Natalie

This recipe for soft Lemon Chia Seed Muffins has the perfect amount of lemon tartness and is so easy to make! The muffins are perfectly delicious for breakfast, a snack or dessert! 

5 from 11 votes

Print Recipe Pin Recipe

Prep Time 20 minutes mins

Cook Time 17 minutes mins

Total Time 37 minutes mins

Course Breakfast, brunch, Muffins

Cuisine American

Servings 12 muffins

Calories 202 kcal

Ingredients

 

0.5x1x2x

• ▢ 1¾ cups (218.75 g) all purpose flour swap in half whole wheat flour if you like
• ▢ 1½ teaspoons baking powder
• ▢ 1/2 teaspoon baking soda
• ▢ 1/2 teaspoon salt
• ▢ 2½ tablespoons (30 g) chia seeds
• ▢ ¼ cup (59.15 ml) avocado oil
• ▢ ½ cup (169.5 g) honey
• ▢ 2 tablespoons lemon zest
• ▢ 1½ tablespoons lemon juice
• ▢ 2 large eggs room temperature
• ▢ ¾ cup (170 g) Greek yogurt full fat or 2%, plain or vanilla, room temperature
• ▢ 1 teaspoon vanilla extract

Optional Topping

• ▢ extra lemon zest optional, about 1/4 of a lemon rubbed into turbinado sugar, for the topping
• ▢ Turbinado sugar optional, about 1 tablespoon, for the topping

Optional Lemon Icing

• ▢ 1/2 cup (60 g) powdered sugar
• ▢ 1 tablespoon lemon juice

Instructions

 

Lemon Chia Muffins

• Preheat oven to 350 F. Line a 12-count muffin pan with cupcake liners.
• In a large bowl whisk to combine the flour, baking powder, baking soda, chia seeds, and salt. 
• To a medium sized bowl, add the avocado oil, lemon zest, Greek yogurt, honey, vanilla extract, eggs, and lemon juice. Whisk to combine. 
• Stir the wet ingredients into the dry ingredients until just combined. Do not overmix. Use an ice cream scoop to evenly distribute the batter (each one about 3/4 full) into the prepared muffin pan.

  (Optional topping: Mix the extra lemon zest and turbinado sugar together in a small bowl and sprinkle it evenly over the muffin tops).
• Bake 15-17 minutes or until a toothpick comes out without wet crumbs when inserted in the middle of a muffin.
• Let cool in the pan for 5-10 minutes then transfer muffins to a wire rack to cool completely. Once cooled, drizzle with icing, if desired. 

Lemon Icing (optional)

• In a medium sized bowl, stir together the powdered sugar and the lemon juice. Add up to a half tablespoon more lemon juice if icing is too thick. Spread or drizzle over the cooled muffins. 

Notes

Original recipe: This recipe was modified in January 2026. To make the original version, use the following: 7 tablespoons (98g) melted, slightly cooled butter (instead of avocado oil), 3/4 cup plus 2 tablespoons granulated sugar (instead of 1/2 cup honey), 1 egg (instead of 2), 1 cup sour cream or Greek yogurt (instead of 3/4 cup Greek yogurt). 

Avoid overmixing: Stir together the wet and dry ingredients until just combined. Avoid overmixing. 

Honey: Instead of honey, swap in 1/2 cup maple syrup or 2/3 cup granulated sugar (if using granulated sugar, add 2-3 tablespoons milk to compensate for moisture).

Greek yogurt: I use whole fat plain Greek yogurt.  You can also use 2% and or vanilla Greek yogurt. 

Nutrition

Serving: 1muffinCalories: 202kcalCarbohydrates: 33gProtein: 5gFat: 6gSaturated Fat: 1gPolyunsaturated Fat: 1gMonounsaturated Fat: 4gTrans Fat: 0.01gCholesterol: 28mgSodium: 212mgPotassium: 70mgFiber: 1gSugar: 17gVitamin A: 43IUVitamin C: 3mgCalcium: 68mgIron: 1mg

Please note that nutritional values are created by an online calculator and should only be used as an estimate.

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