Preheat oven to 425F. Add coconut sugar and coconut oil to a stand mixer bowl or large bowl. Mix until well incorporated.
Add in the eggs, one at a time until fully incorporated. Add in yogurt and vanilla extract to wet ingredients and mix well.
Add in 1/3 cup of applesauce or milk. You will add in the other 1/3 later if batter is too dry.
In a separate bowl, mix or sift together the gluten free flour, baking soda and salt. Add the dry ingredients to the bowl of wet ingredients in three parts, mixing slowly each time.
If the batter seems to dry, add in either more applesauce or almond milk, starting with a bit and adding until you get a nice moist (but not wet) dough consistency. Fold in chocolate chips.
Line a muffin tin with silicone muffin liners and spray them with coconut oil spray. Scoop the batter into the liners with a cookie scoop and place in the oven.
Bake muffins at 425F for 5 minutes. Reduce heat to 350F and bake for an additional 20-25 minutes or until a toothpick comes out clean.