Olive mill by-products are effluents generated during olive oil production process. The two-phase centrifugation system produces a semi-solid olive pomace called “alperujo.” This by-product is a combination of liquid and solid wastes derived from the three-phase manufacturing process. A direct and fast analytical method by ultra-high-performance liquid chromatography-DAD coupled with ESI/MS-MS has been developed for the profiling of phenolic compounds. Thirty-five metabolites belonging to phenyl alcohols, secoiridoids, flavonoids, and iridoids were identified as the main constituents of alperujo in 12 min, including p-coumaroyl aldarate and a verbascoside derivative found for the first time in alperujo and a new ligstroside derivative. Six quantitatively significant components were determined at concentrations ranging from 17.7 mg/L for p-coumaric acid to 370.7 mg/L for hydroxytyrosol. Our data confirm that alperujo is an interesting source of phenolic compounds that could be extracted for use as nutraceuticals.