The simultaneous screening of multiple enzyme activities in a single assay has numerous advantages over the traditional format, since it decreases sampling errors, allows savings in reagents and consumables and reduces the time and labor required to conduct the assays. In the present study, a direct and sensitive assay for the simultaneous detection of epoxide hydrolase and esterase (or lipase) activities was developed. Signal overlap is avoided by synthesizing fluorogenic probes with enzyme-specific alkyl linkers, connected to different fluorophores (resorfurin and umbelliferone), which exhibit emission spectra at different wavelengths. The simultaneous assays were conducted in microplate format with the fluorogenic probes monitored in the same well that uses microorganisms as enzyme source. Our results show that the fluorescent signal from each of the probes used here can be discriminated, allowing multiple enzyme activity detection and quantitation.