Many strategies are used to quantify microbial (poly)phenol metabolites (MPMs) in urine. Currently, to obtain accurate results, the use of phase II conjugate analytical standards is deemed to be the gold standard. However, these standards are expensive or commercially unavailable. Quantification using an affordable and commercially available unconjugated analytical standard following hydrolysis with the crude preparation from Helix pomatia containing arylsulfatase and β-glucuronidase was once considered to be an alternative, but previous studies have shown poor hydrolysis efficiency for conjugated MPMs. In this work, we evaluated the efficiency of purified recombinant enzymes and compared them with the preparation from H. pomatia using 75 urine samples. 38 conjugated MPMs were identified before hydrolysis, associated with 17 unconjugated MPMs. Rapid chemical synthesis of sulfated compounds was carried out to increase the confidence level for the identification of 13 sulfated MPMs. Recombinant enzymes had a mean hydrolysis efficiency of over 95% for 36 out of 38 conjugated MPMs with a hydrolysis time of 30 min. In comparison, the preparation from H. pomatia achieved similar efficiency for only 28 conjugated MPMs after 6 h of hydrolysis. When comparing the concentration of unconjugated MPMs released after enzymatic hydrolysis, recombinant enzymes were more or as effective for almost every MPM. These results demonstrate that accurate quantification of MPMs in urine can be quickly achieved using purified recombinant enzymes and represent an affordable alternative to the use of conjugated analytical standards, improving access to the analysis of the metabolism of (poly)phenols by the gut microbiota.