The aim of the present work was to develop a reproducible, sensitive, and rapid UPLC-ESI-TQ MS analytical method for determination of microbial phenolic acids and other related compounds in faeces. A total of 47 phenolic compounds including hydroxyphenylpropionic, hydroxyphenylacetic, hydroxycinnamic, hydroxybenzoic, and hydroxymandelic acids and simple phenols were considered. To prepare an optimum pool standard solution, analytes were classified in 5 different groups with different starting concentrations according to their MS response. The developed UPLC method allowed a high resolution of the pool standard solution within an 18 min injection run time. The LOD of phenolic compounds ranged from 0.001 to 0.107 μg/mL and LOQ from 0.003 to 0.233 μg/mL. The method precision met acceptance criteria (<15% RSD) for all analytes, and accuracy was >80%. The method was applied to faecal samples collected before and after the intake of a flavan-3-ol supplement by a healthy volunteer. Both external and internal calibration methods were considered for quantification purposes, using 4-hydroxybenzoic-2,3,4,5-d4 acid as internal standard. For most analytes and samples, the level of microbial phenolic acids did not differ by using one or another calibration method. The results revealed an increase in protocatechuic, syringic, benzoic, p-coumaric, phenylpropionic, 3-hydroxyphenylacetic, and 3-hydroxyphenylpropionic acids, although differences due to the intake were only significant for the latter compound. In conclusion, the UPLC-DAD-ESI-TQ MS method developed is suitable for targeted analysis of microbial-derived phenolic metabolites in faecal samples from human intervention or in vitro fermentation studies, which requires high sensitivity and throughput.