Mix eggs, sugar, melted butter, Greek yogurt, and vanilla extract together in a bowl with an electric mixer until smooth and creamy. Add flour mixture into the wet ingredients and mix until well combined, but be careful not to overmix.
Toss 3/4 cup of the chocolate chips with 1 tablespoon almond flour in a bowl so that the chips are lightly coated. Fold the coated chocolate chips into the batter. Distribute the batter evenly between 10 paper-lined muffin cups, filling the cups all the way to the top. Sprinkle remaining chocolate chips over the tops of the muffins.
Bake in a preheated oven for 5 minutes, then reduce heat to 350 degrees F (175 degrees C). Continue baking until the tops are golden and a toothpick inserted into the center of one of the muffins comes out clean, 12 to 15 minutes.
Cool muffins in the pan on a wire rack for at least 5 minutes before serving.
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