Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5′ monophosphorylated mRNA decay intermediates (5′P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5′–3′ exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5′–3′ exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5′P degradome) sequencing approach, we characterize 5′P mRNA decay intermediates in 96 species includingBacillus subtilis,Escherichia coli,Synechocystisspp. andPrevotella copriand identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5′P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.