Preheat the oven to 425°F (220°C). Line a standard 12-cup muffin pan with parchment paper muffin liners.
In a large mixing bowl, whisk together the eggs, sour cream, milk, oil, and vanilla extract until smooth and fully combined. This should take about 30–60 seconds.
Add the brown sugar and granulated sugar to the wet ingredients and whisk again until the mixture is creamy and the sugars begin to dissolve.
In a separate medium bowl, whisk together the gluten-free flour, cocoa powder, baking powder, baking soda, xanthan gum (if using), and salt. Make sure the cocoa is well incorporated to avoid streaks.
Pour the dry ingredients into the wet ingredients in the large bowl. Use a spatula or wooden spoon to gently stir until just combined. Do not overmix—some small lumps are okay. Overmixing can create dense muffins.
Fold in 3/4 cup of the chocolate chips or chunks using a spatula, reserving the remaining 1/4 cup for topping.
Let the batter sit for 20-30 minutes to get the activators bubbly!
Using a large muffin scoop or 1/4 cup measure, portion the batter into the prepared muffin tin, filling each cup nearly to the top. Sprinkle the remaining chocolate chips or chunks on top of each muffin.
Bake muffins at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 13–15 minutes or until a toothpick inserted into the center comes out with moist crumbs (not wet batter). Do not open the oven door when lowering the temperature—just adjust the dial.
Let the muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely. This helps them set and prevents sogginess.