A diformyl-quinoline based receptor (L1) exhibits selective colorimetric and fluorometric sensing of Zn2+ in aqueous medium at pH 7.4 based on ICT process. The in situ formed phenoxo-bridged complex, L1.2Zn can selectively and specifically sense PPi among all the other biologically important anions including ATP through reversible binding. The detection limit for Zn2+ and PPi were found to be approximately 56 ppb and 2 ppb respectively. The unique selectivity of the PPi by L1-Zn ensemble could be used as an analytical tool to probe PPi generation in a prototype PCR setup and track DNA amplification with higher sensitivity as compared to conventional agarose gel electrophoresis. Interestingly, the principle of PPi estimation in PCR rendered rapid estimation of bacterial cell numbers with a limit of detection of 10 CFU of E.coli MTCC 433 in as early 10 PCR cycles. The proposed method of PPi sensing offers interesting application potential in PCR-based rapid diagnostics for pathogenic agents and microbiological quality control.