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You are here: Home / Recipes / Breakfast / Healthy Lemon Chia Seed Muffins

Healthy Lemon Chia Seed Muffins

Dairy FreeVegan

August 7, 2018 8 Comments

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These Healthy Lemon Chia Seed Muffins are the perfect breakfast! Low in sugar and vegan, they’re packed with zesty lemon flavor and nutritious chia seeds. 

Healthy Lemon Chia Seed Muffins

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These Healthy Lemon Chia Seed Muffins are basically like a ray of sunshine in muffin form. I swear I could eat them for breakfast every day!

They’ve got the perfect amount of zesty lemon, protein and omega 3’s from the chia seeds, and just taste SO yummy! I came up with this recipe years ago when we first moved into our apartment, and it’s been one of my favorites ever since.

This week, I’ve teamed up with tons of different bloggers for Muffin Week 2018! You’ll find all kinds of muffins (sweet + savory!) from lots of other talented food bloggers here like these Healthy Lemon Blueberry Muffins or No Sugar Added Pumpkin Zucchini Muffins… yum!

Lemon Chia Muffins

On the first night we were in our new apartment together (and ate popcorn for dinner on top of a moving box) I promised Tyler I would make him whatever he wanted for breakfast to make up for our lack of exciting dinner.

He quickly replied – Lemon Poppyseed Muffins. Buuuut… when I went to look in the cabinet we didn’t have poppy seeds. (Because who thinks to buy poppy seeds for your new apartment when you’re hungry, tired and grocery shopping at 9’o clock on a Saturday night)

I didn’t want to crush his hopes and deny the request, so I just agreed and figured I’d come up with something in the morning.

Click here to pin this recipe for later.

Healthy Lemon Chia Muffins

When I was getting out the ingredients to bake the muffins, I noticed I had a big bag of chia seeds in our pantry that would be PERFECT as a replacement for the poppy seeds. I’m kinda in love with chia seeds.

Even though they’re little – they’re tiny powerhouses! Just one tablespoon of them has 4g of fiber, 3g of protein and more than a third of your daily recommended intake of omega 3 fatty acids!

What makes these muffins healthy?

  • Healthy whole grains – The base of these muffins is a combo of oat and whole wheat flour! Usually muffins are made with white flour, but the whole grains help make this a healthier muffin that will keep you fuller for longer!
  • Low sugar – Rather than loading these muffins up with sugar, I sweetened them with just maple syrup

Vegan Lemon Chia Seed MuffinsBack to the muffins… So I subbed in chia seeds for the usual poppy seeds…. and Tyler gave them the stamp of approval. I think you’ll love them just as much!

They’re a little tangy from the lemon, perfectly sweet from honey, and have a little superfood crunch thanks to the chia seeds. You’re gonna love them!

Substitutions for these Healthy Lemon Chia Seed Muffins:

  • If you don’t want to flax eggs you can use 2 regular 
  • If you don’t have flax seed meal, you can pulse flax seeds in a food processor or blender until they are fine.
  • You can sub maple syrup with honey
  • I haven’t tried making these muffins gluten free, but you may be able to substitute whole wheat flour with gluten free flour

Healthy Lemon Chia Muffins

Love muffins? Try these healthy muffin recipes!

  • Healthy Apple Muffins
  • Healthy Banana Protein Muffins
  • Healthy Carrot Pineapple Muffins
  • Healthy Cranberry Orange Muffins
Healthy Lemon Chia Seed Muffins
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5 from 3 votes

Healthy Lemon Chia Seed Muffins

These Healthy Lemon Chia Seed Muffins are the perfect breakfast! Low in sugar and vegan, they're packed with zesty lemon flavor and nutritious chia seeds.
Course Breakfast
Cuisine American
Keyword healthy lemon chia seed muffins, lemon chia seed muffins
Prep Time 10 minutes
Cook Time 15 minutes
Total Time 25 minutes
Servings 16 muffins
Calories 117kcal

Ingredients

For flax egg:

  • 3 tablespoons flax seed meal
  • 7.5 tablespoons warm water

For the batter:

  • 2 ½ tablespoons lemon zest
  • 6 tablespoons lemon juice freshly squeezed
  • 1 tablespoon coconut oil melted + cooled
  • ½ cup applesauce
  • 4 tablespoons maple syrup
  • 1 cup almond milk
  • 1.5 cup oat flour
  • 1 cup whole wheat pastry flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon cinnamon
  • 3 tablespoons chia seeds

Instructions

  • Preheat oven to 350 and prepare a greased or lined muffin tin.
  • In a small bowl, mix together flax seed meal and warm water until combined. Allow them to sit for 5 minutes and solidify to make 'flax eggs'.
  • In a bowl combine flax eggs, lemon zest, lemon juice, oil, applesauce, maple syrup and almond milk
  • Stir in flours, baking powder, baking soda, cinnamon + chia seeds.
  • Pour batter in to greased muffin tins
  • Bake for 20 minutes until edges are golden brown and toothpick comes out clean when inserted inside.

Notes

Substitutions for these Healthy Lemon Chia Seed Muffins:
  • If you don't want to flax eggs you can use 2 regular 
  • If you don't have flax seed meal, you can pulse flax seeds in a food processor or blender until they are fine.
  • You can sub maple syrup with honey
  • I haven't tried making these muffins gluten free, but you may be able to substitute whole wheat flour with gluten free flour

Nutrition Facts

Nutrition Facts
Healthy Lemon Chia Seed Muffins
Amount Per Serving (1 muffin)
Calories 117 Calories from Fat 27
% Daily Value*
Total Fat 3g 5%
Saturated Fat 1g 5%
Sodium 93mg 4%
Potassium 136mg 4%
Total Carbohydrates 19g 6%
Dietary Fiber 2g 8%
Sugars 4g
Protein 3g 6%
Vitamin C 4.2%
Calcium 6.3%
Iron 5.6%
* Percent Daily Values are based on a 2000 calorie diet.
Looking for help with eating healthy?Check out our 4 Weeks of Clean Eating Guide!
Tried this recipe?Share it! Make sure to tag @thecleaneatingcouple or use #thecleaneatingcouple!

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Filed Under: Breakfast, Dairy Free, Recipes, Snacks, Vegan

Previous Post: « Sheet Pan Maple Mustard Pork Tenderloin Dinner
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Reader Interactions

Comments

  1. Emily

    October 12, 2016 at 2:25 pm

    They look so perfectly peaked and really yummy; I love the fresh taste of lemons and poppy seeds in muffins.
    Emily recently posted…Apple White Chocolate Caramel Bars + A Giveaway Announcement!My Profile

    Reply
    • The Clean Eating Couple

      October 12, 2016 at 3:36 pm

      It’s baking soda! My secret weapon 🙂 Lemons in any baked good are great!

      Reply
  2. Jenna @ A Savory Feast

    August 7, 2018 at 1:44 pm


    I have a ton of chia seeds I need to find more ways to use, so I can’t wait to try this! Love a healthy muffin recipe.

    Reply
    • The Clean Eating Couple

      August 8, 2018 at 11:50 am

      Thanks girl! I can’t wait to try the pumpkin zucchini muffins you posted about!!

      Reply
  3. Ali Baldwin

    October 26, 2018 at 2:11 pm


    Love love love these! My family devours them whenever I make them!

    Reply
    • The Clean Eating Couple

      October 27, 2018 at 7:34 am

      That makes me so happy to hear, Ali!! Love that your whole family loves them 🙂

      Reply
  4. Dani

    February 20, 2019 at 8:47 pm


    Really surprised at how fuffy they came out. SUPER simple to make — had all of the ingredients in my apt without having to search for anything crazy. Added collagen peptides to make them even extra special.

    Reply
    • The Clean Eating Couple

      February 21, 2019 at 7:14 am

      Really glad to hear you liked them Dani!! And that the collagen peptides addition worked out 🙂

      Reply

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