High-quality dark chocolates (70% cocoa content) can have shades from light to dark brown color. This work aimed at revealing compounds that discriminate black and brown chocolates. From 37 fine chocolate samples from years 2019 and 2020 provided by Valrhona,8 dark black samples and 8 light brown samples were selected. A non-targeted metabolomics study was performed based on ultra-high performance liquid chromatography—high resolution mass spectrometry/mass spectrometry experiments, univariate, multivariate, and feature-based molecular networking analyses. Twenty-seven overaccumulated discriminating compounds were found for black chocolates. Among them, glycosylated flavanols including monomers and glycosylated A-type procyanidin dimers and trimers were highly representative. Fifty overaccumulated discriminating compounds were found for brown chocolates. Most of them were B-type procyanidins (from trimers to nonamers). These phenolic compounds may be partially related to the chocolate colors as precursors of colored compounds. This study increases the knowledge on the chemical diversity of dark chocolates by providing new information about the phenolic profiles of black and brown chocolates.