Enterohaemorrhagic E. coli is a significant human pathogen that causes disease ranging from acute diarrhoea to potentially life threatening haemolytic uremic syndrome and renal failure. The type 3 secretion (T3S) system is essential for colonisation in both ruminants (the natural reservoir) and ex vivo human intestinal models. Using transposon mutagenesis we have found that the ybeZYX-Int operon as required for T3S and that the conserved endoribonuclease ybeY is responsible for this effect. YbeY matures the 3’ end of 16S rRNA and degrades defective 70S ribosomes. In the absence of YbeY, mature 70S ribosomes are depleted. We find that the EHEC ∆ybeY strain is also temperature sensitive and has reduced motility. In Vibrio cholerae and Yersinia enterocolitica, deletion of ybeY alters virulence gene expression and this has been linked with YbeY processing of small RNAs. Using UV-crosslinking and RNA sequencing we present evidence that YbeY binds the “neck” and “beak” of 16S rRNA and, contrary to a growing body of literature, does not bind small RNAs. Using sub-inhibitory concentrations of the translation initiation inhibitor, kasugamycin, we find that the polycistronic mRNAs that encode the T3S system are rapidly degraded in the absence of translating ribosomes, inhibiting T3S. Our results demonstrate that type 3 secretion is particularly sensitive to depletion of initiating ribosomes and explains the observed inhibition of T3S in the ∆ybeY strain. We propose that many of the pleiotropic effects observed in V. cholerae and Y. enterocolitica ybeY mutants are not due to changes in small RNA regulation, but are due to global changes in mRNA stability when protective ribosomes are depleted.