In most microorganisms studied to date, utilisation of phosphonate is induced under conditions of inorganic phosphate limitation, and the enzymes of phosphonate catabolism are encoded by orthologous genes. Four phosphonate breakdown pathways are known which differ in their substrate specificity and cleavage mechanisms. The degradation of phosphonates by common microbial pathogens belonging to 22 microbial species grown in phosphate-rich media was investigated employing nuclear magnetic resonance spectroscopy and bioinformatic searches. Fifteen bacterial and four fungal species were capable of cleaving phosphonate (C-P) bonds of α-aminomethylphosphonate, phosphonoacetate or phenylphosphonate, indicating that the enzymes responsible for these activities are expressed in the absence of phosphorus limitation. In silico analyses indicated that most of the microorganisms with phosphonate degradation activities did not have genes orthologous to those encoding C-P cleaving enzymes of the classical phosphonate catabolism pathways. The results suggested that phosphonate degradation in some bacteria and fungi, including human and animal pathogens, took place via novel pathways. These metabolic characteristics can be exploited to design potent antimicrobial pro-drugs bearing phosphonate moieties that would be cleaved off when taken up by microorganisms releasing the active drug.