Lemon Chia Seed Muffins

These Lemon Chia Seed Muffins are an easy healthy on the go muffin. Perfect for a mid-morning snack or grab and go breakfast.

muffins stacked with a bite taken out

Made with half whole wheat flour and half white flour for additional fiber, chia seeds for omega-3 fatty acids, and lemon juice for bright zesty flavor!

Add the lemon glaze on top for extra sweetness. These muffins are not super sweet, so if you like your muffins on the sweet side definitely add a little extra sugar to the batter or try the lemon glaze on top!

Instructions and Steps

Here is the layout of steps. The most important step, and fun if you ask me, is the lemon zest and sugar step!

Start by adding your sugar and freshly zested lemons to a food processor. Pulse until the zest is finely ground up and blends into the sugar.

It will smell heavenly!

While you don’t have to blend the zest and sugar together, I find it helps release the natural aroma and oils well. And we’re going for the zestiest and lemony muffins, right?!

sugar and lemon zest blended in a food processor

So, if you decide to go with the critical step of blending the sugar and zest together, set it aside for later. You’ll add it to the dry ingredient bowl in a bit.

Next, get two mixing bowls – one for dry ingredients and one for wet ingredients.

wet and dry lemon muffin ingredients

Mix the two bowl’s ingredients together. Then pour the wet ingredients into the dry ones. Mix until just combined. You don’t want to overmix the batter.

Hopefully, your oven is pre-heated, and your muffin tin is ready to go!

Scoop the batter into the muffin tins and bake until a toothpick comes out clean – about 20-25mins.

For these pictures, I halved the batch so we only got 6 muffins, but the recipe makes a dozen.

lemon muffin batter in muffin tins


Enjoy the muffins right away still warm from the oven or store for later!

I love making a batch for easy breakfasts during the week or I take them with me to work as my mid-morning snack.

At room temperature, they’ll last well for 4-5 days. Make sure they’re tightly wrapped so that air doesn’t dry them out.

If you’d rather refrigerate them, they’ll last up to a week. For freezing you’ll be good for 3 months!

freshly baked muffins on a plate

Lemon Glaze

The glaze isn’t necessary, but it does a nice touch of sweetness!

It’s a super simple recipe: melt some butter, mix with powdered sugar and fresh lemon juice and voila – you got a thick icing or glaze that’ll harden well and have good flavor!

lemon chia seed muffins with glaze

Lemon Chia Seed Muffins

Healthy Lemon Chia Seed Muffins with a zesty glaze are a great grab and go snack or breakfast – plus easy to meal prep!
Print Pin Rate
Prep Time: 20 minutes
Cook Time: 20 minutes
Total Time: 40 minutes
Servings: 12 muffins


Muffin Batter

  • 1 cup whole wheat flour
  • 1 cup white flour
  • 2 tablespoons chia seeds
  • 2 teaspoons baking powder
  • 1/2 teaspoon salt
  • 1/2 cup sugar
  • zest of 2 lemons
  • 1/2 cup milk
  • 1/4 cup avocado oil
  • 4 tablespoons melted butter (or 1/4 cup)
  • 1/4 cup lemon juice
  • 2 eggs
  • 1 teaspoon vanilla extract

Lemon Icing

  • 1 cup powdered sugar
  • 1 tablespoon lemon juice
  • 1 tablespoon melted butter


  • Preheat the oven to 350 degrees Fahrenheit.
  • In a large mixing bowl combine the flours, chia seeds, baking powder and salt.
  • In a food processor, pulse the sugar and lemon zest until fragrant.
  • Stir in the sugar and lemon zest into the dry ingredient bowl.
  • In a separate bowl, whisk together the milk, avocado oil, melted butter, lemon juice, eggs and vanilla extract.
  • Add the wet ingredients into the large bowl of dry ingredients and mix just until combined. Careful to not overmix.
  • Bake for 20-25mins or until a toothpick comes out clean.
  • If making the icing, mix the melted butter and lemon juice into the powdered sugar and drizzle on the muffins.


  1. These muffins aren’t overly sweet, so if you prefer your muffins on the sweet side add more sugar to the batter or definitely try the icing on top.
  2. Stores well at room temperature for 4-5 days. Just make sure to wrap the muffins tightly so that they don’t dry out.
  3. Lasts 7 days in the refrigerator.
  4. Store for up to 3 months in the freezer.


Calories: 205kcal | Carbohydrates: 26g | Protein: 4g | Fat: 10g | Saturated Fat: 3g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 5g | Trans Fat: 1g | Cholesterol: 38mg | Sodium: 258mg | Potassium: 89mg | Fiber: 2g | Sugar: 9g | Vitamin A: 178IU | Vitamin C: 3mg | Calcium: 76mg | Iron: 1mg

(Nutrition values are calculated by third-party software and an estimate that can vary based on product brands and cooking methods.)

Course: Breakfast, Snack
Cuisine: American
Keyword: lemon chia seed muffins, healthy lemon muffins
Tried this recipe? I love seeing your creations!Mention @monicanedeff.rdn or tag #monicanedeff so I can share them with the community!

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