Fast protein and metabolite liquid chromatography (FPLMC) was introduced years ago to enable the easy separation of high-molecular compounds such as proteins from small molecules and the identification of the low-molecular substances. In this paper, the method is applied for the rapid evaluation of freshness and monitoring the aging of animal meat and fish. A novel chromatographic sensor was developed with a deep UV LED-based photometric detection unit (255–265 nm), an original flow cuvette and registration scheme; the processing of a chromatogram with the sensor takes approximately 15 min. Strict isochronism between the elution of ATP metabolites, mainly hypoxanthine (Hx) and inosine monophosphate (IMP), and the time of maturation of meat or fish, was discovered. A new freshness index H* = [Hx]/[IMP] was introduced, which is proportional to the instrumental delay time in the FPMLC chromatograms: the H* index < 0.5 indicates the presence of inosine monophosphate (IMP) and the high quality of the meat or fish. Reasonably strong correlations were revealed between data obtained by FPMLC and total volatile basic nitrogen TVB-N (for fish) or volatile fatty acids VFA (for meat) content. Moreover, putative nucleotide salvage and an increase in the concentration of IMP were observed in fish after heat treatment using the FPMLC sensor and NMR technique.