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Preheat oven, prep pan, and melt butter and bitttersweet chocolate: Preheat oven to 350F. Line twelve 2-½-inch muffin cups with paper bake cups. In a heatproof bowl set over (not in) a pot of simmering water, melt butter and bittersweet chocolate, stirring until smooth.
Add sugar: Remove from heat and whisk in sugar.
Add eggs, one at a time: Whisk in eggs, one at a time, until combined.
Add cocoa: Whisk in cocoa and salt.
Add flour: Fold in flour until combined.
Add chocolate chips: Stir in all chocolate chips.
Divide batter between cups and bake: Fill each cup nearly full with batter. Bake until top of brownie cup appears set and edges are slightly puffed, 20-25 minutes. Let brownies cool in pan for 15 minutes. (Center of brownies may dip upon cooling.)
Cool: Transfer to a wire rack and let cool completely.