Chocolate Filled Cookies

Chocolate Filled Cookies- low in sugar, high in protein, and gluten free

These chocolate filled cookies are low in carbs and sugar, are soft and chewy, and are packed with a high protein, gooey chocolate filling. They’re perfect for satisfying the sweetest sweet tooth, but without any of the guilt.

Chocolate Filled Cookies- low in sugar, high in protein, and gluten free

There is something about the sweet surprise of a filling in a cookie that is so satisfying.

Chocolate Filled Cookies- low in sugar, high in protein, and gluten free

And these chocolate filled, soft, chewy cookies are no exception. They’re like eating a cloud filled with chocolate.

Gooey, creamy, melty chocolate…..mmmm.

Chocolate Filled Cookies- low in sugar, high in protein, and gluten free

The cookie is vanilla/almond flavored, reminiscent of a traditional chocolate chip cookie. With healthy fats from the almonds, fiber from the oats, protein from the yogurt and protein powder, you’ve got a perfectly balanced distribution of macronutrients in the palm of your hand (and yes, each cookie is about that big!  😀 )

The chocolate filling tastes just like melted chocolate chips, but is actually high in protein, healthy fats, and low in sugar. It was adapted from my healthy snickers bar recipe, which uses it as the coating for the bars. Healthy chocolate?! Yes, please!

These cookies are naturally gluten free and can easily be made vegan.

They may taste indulgent, but they are full of good for you, nutritious ingredients! Just take a bite and see for yourself!

Yields 12 cookies

Chocolate Filled Cookies

Vegan - optional; Gluten Free; Lower Sugar; High Protein; Egg Free; Soy Free

40 minPrep Time

5 minCook Time

45 minTotal Time

Recipe Image
Save RecipeSave Recipe


  • 1 ½ Tbsp coconut oil
  • ½ cup unsweetened cocoa powder (dark or regular)
  • 1/3 cup chocolate or unflavored protein powder of choice (any type – I used unflavored hemp)
  • 1 ½ Tbsp granulated sweetener of choice
  • ¼ tsp salt
  • ¼ cup + 1 Tbsp milk of choice
  • 2 Tbsp water
  • ½ tsp vanilla extract
  • Cookies
  • 1 Tbsp flaxseed meal
  • 2 Tbsp water
  • 1 cup brown rice flour
  • ½ cup almond flour
  • ½ cup coconut flour
  • ¼ cup oat flour
  • 1/8 cup granulated sweetener of choice (I used regular granulated sugar)
  • 1 ½ tsp cream of tartar
  • 1 tsp baking soda
  • ¼ tsp salt
  • ½ cup plain or vanilla yogurt (dairy or dairy-free - I used plain nonfat Siggi’s Icelandic yogurt)
  • ¼ cup unsweetened applesauce
  • 1/8 cup honey or agave (I used agave)
  • 1/8 cup coconut oil
  • 3 Tbsp milk of choice
  • 1 tsp almond extract
  • 1 tsp vanilla extract
  • 1 tsp apple cider vinegar


  1. Preheat the oven to 350 F and grease or line with parchment paper a cookie sheet pan.
  2. For the filling: if needed, melt the coconut oil until it’s in a liquid state.
  3. In a medium bowl, combine the cocoa powder, protein powder, sweetener, and salt.
  4. Stir in the coconut oil, milk, water, and vanilla until fully incorporated into the dry ingredients.
  5. For the cookies: In a small bowl, combine the flaxseed meal and water to make a “flax egg”. Set aside.
  6. In a large bowl, combine the flours, sweetener, cream of tartar, baking soda, and salt.
  7. In a separate bowl, combine the yogurt, applesauce, honey or agave, oil, milk, extracts, and vinegar. Stir to combine.
  8. Add the flax egg to the wet ingredients. Stir until fully incorporated.
  9. Add the wet ingredients to the dry and stir until combined.
  10. Scoop out dough 1 Tbsp at a time. Roll the dough into a ball then press it between your hands to flatten to about ¼” thick. (Note: if any liquid comes out of the dough when pressed, it is too moist and you can add a 1 Tbsp of any flour at a time until no liquid comes out of the dough when pressed)
  11. With your thumb, press a small indenture in the center of the dough.
  12. Fill the dent with about 1-2 tsp chocolate filling.
  13. Take another flattened piece of cookie dough and place it on top of the filled dough. Pinch the edges of the two pieces together, then roll into a ball.
  14. Place filled cookies onto prepared cookie tray. Cookies won’t spread, but still place them at least 1 inch apart.
  15. Bake for 5-6 minutes, or until the cookies just begin to firm up. Let them cool on the tray.
  16. Then you’re ready to eat!

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.