During protein maturation, post-translational proteolytic processing events sculpt the proteome by cleaving single or secretion signals from the polypeptide chain, generating new proteoforms. Mycoplasma hyopneumoniae is a genome-reduced, porcine respiratory pathogen responsible for severe economic losses to swine production. We have characterised proteolytic events in key adhesin families, that occur at defined sites which are essential to the formation of functional, mature proteoforms on the extracellular surface of the organism. Some of these N-terminal processing events are performed by the ubiquitous methionine aminopeptidase (MAP) enzyme which removes the first methionine when the proceeding amino acids are small, in a manner that follows the N-end rule common to most organisms. To explore the extent of proteolytic processing we took an untargeted, high-throughput approach to identify neo-N-termini in the proteome of M. hyopneumoniae. Using protein dimethyl-labelling, reversed-charge enrichment of N-termini and mass spectrometry, 672 N-terminal sequences were characterised. Our data verified 74 protein start sites and identified the precise location of post-translational proteolytic cleavage events in 58 functionally-diverse proteins. Many of the protein N-termini identified adhere to the N-end rule, however we observed cleavage events which did not follow the N-end rule. We propose that other aminopeptidases, which are present in M. hyopneumoniae, are responsible for the removal of methionine in these proteins and contribute to the diversity of processing events in this important agricultural pathogen. We tested this hypothesis by assessing the ability of recombinant aminopeptidases to remove methionine from a panel of synthetic peptides with different amino acids in position two. Endoproteolytic cleavage sites were also identified in 35 proteins with well-defined, canonical functions in the cytosol. These observations suggest that microbial N-terminal processing of proteins is more complex and widespread than previously thought.