The pathogen Vibrio cholerae modulates the expression of many genes in order to transition from its environmental reservoir to its niche in the human host. Among these are genes encoding two related Type IV pili, the mannose-sensitive haemagglutinin (MSHA) pilus, which aids V. cholerae persistence in aquatic environments but causes clearance of bacteria by host immune defences, and the toxin co-regulated pilus (TCP) required for colonization. These antagonistic effects are resolved transcriptionally by the regulator ToxT, which represses msh genes while activating tcp genes during infection. We show that these two pili systems are also intertwined post-transcriptionally through the ToxT-regulated pre-pilin peptidase TcpJ. We found that the major MSHA pilin, MshA, was degraded in V. cholerae in a TcpJ-dependent fashion. In a heterologous Escherichia coli system, TcpJ can recognize both MshA and its cognate substrate, the TCP subunit TcpA, but that processing by TcpJ causes the degradation of MshA. Through site-directed mutagenesis and chimeric pilin analysis, we show that this process targets a combination of MshA N-terminal motifs and depends on the proteolytic activity of TcpJ. Moreover, overexpression of tcpJ partially restored the ability of bacteria unable to transcriptionally downregulate msh genes to colonize infant mice. These findings describe co-ordinated proteolysis as a regulatory mechanism in V. cholerae and illustrate this organism's adaptability in the face of dramatic environmental changes.