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Preheat the oven to 375 ºF and position the rack in the middle of the oven.
Line a 12-hole muffin tin with paper liners.
In a large bowl, combine gluten-free flour, almond flour, brown sugar, baking powder, baking soda, xanthan gum, and salt.
Add butter to the dry ingredients and mix with a hand or standing mixer until the mixture resembles breadcrumbs.
Gradually add the milk, yogurt, eggs, vanilla extract to the butter-flour mixture and whisk until a thick, smooth batter forms without flour clumping.
Add 1 tbsp of the gluten free muffin batter to the bottom of each muffin liner. This will help prevent the chocolate chips from sinking all the way to the bottom.
Stir in chocolate chips into the batter, reserving some for sprinkling on top, until evenly distributed.
Divide the rest of the batter equally into the muffin cases, filling them to the brim for standard muffins or creating a small mound above the edge for jumbo muffins. Sprinkle with reserved chocolate chips and a bit of sugar.
Bake at 375 ºF for 20-22 minutes until the muffins rise, turn golden brown, and a toothpick comes out clean or with a few moist crumbs.
Let the muffins cool in the tin for 5 minutes, then transfer them to a wire cooling rack to cool completely.