YbeX of Escherichia coli, a member of the CorC protein family, is a putative Co ²⁺/ Mg ²⁺ efflux factor. Here, we describe several ΔybeX phenotypes and report an involvement of YbeX in ribosomal metabolism. E. coli lacking ybeX has a longer lag phase on outgrowth from the stationary phase. This phenotype is heterogeneous at the individual cell level and can be rescued by supplementing the growth media with magnesium. ∆ybeX strain is sensitive to elevated growth temperatures and to several ribosome-targeting antibiotics, which have a common ability to induce the cold shock response in E. coli. ∆ybeX cells accumulate distinct 16S rRNA degradation intermediates present in both 30S particles and 70S ribosomes. We propose that a function of YbeX is maintaining the magnesium homeostasis in the cell, which is needed for proper ribosomal assembly.