Lemon Chia Seed Protein Cookies | Amy's Healthy Baking (2024)

Soft & chewy cookies full of bright, sunshiny lemon flavor. They’re packed with protein & extra nutrients, so they’re healthy enough for breakfast!


I grew up going to church every Sunday with my parents. As early birds, we usually went to the 8:15 am service instead of the one held later at 10 am. With a community full of people who enjoyed sleeping in, the sanctuary was normally fairly empty at that hour!

But during the summers, the church only offered one service at 9:30 am to give the pastors a “summer break…” Or at least the ability to sleep in too! So the building filled up to the seams, threatening to burst open, with all of us rambunctious kids squirming in our seats.

After the first 10 minutes and the Children’s Moment, we were excused to run out the doors and into the adjoining hall, where a few very patient people held a children’s worship for us. We spent the rest of the hour coloring, singing, and playing games, which allowed the adults time to listen to the regular sermon in peace and quiet.


Besides the coloring, my favorite part of the summers at church was the special brunch held after the service. Different members would bring in trays of goodies: fresh fruit and veggies, cucumber sandwiches, deviled eggs, muffins, donuts, and sometimes even cookies.

Yes, donuts and cookies! You can probably guess what I filled up my plate with… Mom always reminded us that the “cookies for breakfast” treat was a special occasion and not something that would regularly occur at home, but…


Even now, I sometimes think about cookies for breakfast. (Same with crumbles—but those are mostly fruit and granola anyway, right?) So I came up with these Lemon ChiaSeed Protein Cookies as a compromise. They taste just like dessert but are packed with nutrients and protein, so they’re actually healthy enough for breakfast!


These special cookies have 3 things that make them healthy enough for your morning meal.

1) Low carb. I used coconut flour instead of all-purpose in these cookies. It’s much more absorbent that regular flour, so you’ll only use a third of the amount. That really helps cut out carbs! I also use a combination of agave and no-calorie plant-based sweeteners, so you won’t experience the same sugar high (and crash) as with regular cookies.

2) Protein powder. Since I still had lots left over from these healthy muffins, I used a few scoops of this protein powder as the other half of the dry ingredients. It has a sweet vanilla taste and no strange flavors. I promise you can’t tell—they taste just like regular, sunshiny lemon cookies!


3) Chia seeds. For an extra nutritious boost, I added a tablespoon of chia seeds to the cookie dough. They’re full of fiber, antioxidants, and omega-3’s, as well as other micronutrients, and the cookies are a fun way to sneak all of that in!


Because both the coconut flour and chia seeds are fairly absorbent, the cookies don’t spread during baking, so it’s important to flatten the cookie dough to your preferred thickness and width before popping the pan in the oven. If you prefer thicker cookies, they may need a minute or two more than the bake time called for in the recipe.


Just look at these sweet, sunshiny beauties! And the fact that they’re healthy enough for breakfast? Yeah… I’m probably not sharing a single one. 😉

Lemon Chia Seed Protein Cookies

4.8 from 13 reviews

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©: Amy's Healthy Baking

Yields: 12 cookies

These healthy cookies are supremely soft and chewy. They’re a lemon-lover’s dream! Store any leftovers in an airtight container for up to 5 days.

  • ¼ cup (28g) coconut flour (measured correctly)
  • 2 scoops (84g) vanilla whey protein powder (I used Jamie Eason's Lean Body for Her — see Notes!)
  • ¾ tsp baking powder
  • ½ tsp xanthan gum
  • ¼ tsp salt
  • 1 tbsp (15g) chia seeds
  • 1 tbsp (3g) lemon zest (about 1 medium)
  • 1 ½ tbsp (21g) coconut oil or unsalted butter, melted and cooled slightly
  • 1 large egg, room temperature
  • 1 tsp vanilla extract
  • 3 tbsp (45mL) freshly squeezed lemon juice (about 1 medium)
  • ¼ cup (60mL) agave
  • 2 tbsp Swerve
  • 2 tbsp Truvia
  1. In a small bowl, whisk together the coconut flour, protein powder, baking powder, xanthan gum, salt, chia seeds, and zest. In a separate bowl, whisk together the coconut oil, egg, and vanilla. Stir in the lemon juice and agave. Mix in the Swerve and Truvia until completely dissolved. Stir in the coconut flour mixture until completely incorporated. Let the cookie dough rest for at least 10 minutes.
  2. While the cookie dough rests, preheat the oven to 325°F, and line a baking sheet with parchment paper or a silicone baking mat.
  3. Drop the cookie dough into 12 rounded scoops onto the prepared baking sheet, and flatten to the desired thickness and width. (Between ¼” to ½” is best.) Bake at 325°F for 11-13 minutes. Cool the cookies on the baking sheet for at least 10 minutes before turning out onto a wire rack.

Notes: I have only tried making these cookies with this protein powder. Unfortunately, it's no longer sold in stores, but this one is from the same parent company, almost exactly identical to the one I used, and my top recommendation as a substitute!

Not all protein powders absorb liquids equally. If the cookie dough looks too dry, add 2 teaspoons of milk at a time until everything comes together. If it looks too wet after letting it rest, add 1 teaspoon of coconut flour at a time until the texture is thicker.

Xanthan gum helps hold the cookies together and make them chewy.

Swerve and Truvia are both no-calorie, Stevia-based sweeteners. You may use all of one or the other, or you may substitute your preferred granulated sweetener instead.

For more tips and answers to all other questions, including substitutions, see my .

{gluten-free, clean eating, low fat, low calorie, low carb, high protein}

View Nutrition Information + Weight Watchers Points

You may also like Amy’s other recipes…

Lemon Poppy Seed Protein Muffins

Lemon Poppy Seed Loaf Cake

Cran-Raspberry Lemonade Protein Smoothie

Lemon Chia Seed Protein Cookies | Amy's Healthy Baking (2024)

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