mRNAs can fold into complex structures that regulate gene expression. Resolving such structures de novo has remained challenging and has limited our understanding of the prevalence and functions of mRNA structure. We use SHAPE-MaP experiments in living E. coli cells to derive quantitative, nucleotide-resolution structure models for 194 endogenous transcripts encompassing approximately 400 genes. Individual mRNAs have exceptionally diverse architectures, and most contain well-defined structures. Active translation destabilizes mRNA structure in cells. Nevertheless, mRNA structure remains similar between in-cell and cell-free environments, indicating broad potential for structure-mediated gene regulation. We find that the translation efficiency of endogenous genes is regulated by unfolding kinetics of structures overlapping the ribosome binding site. We discover conserved structured elements in 35% of UTRs, several of which we validate as novel protein binding motifs. RNA structure regulates every gene studied here in a meaningful way, implying that most functional structures remain to be discovered. Display omitted •E. coli mRNAs adopt highly diverse and complex structures•Translation is the main source of mRNA structural destabilization in cells•Translation efficiency is strongly correlated with ribosome-binding-site structure•Conserved structured elements found in 35% of UTRs High-resolution probing of hundreds of genes in living E. coli cells reveals that bacterial mRNAs fold into highly diverse and complex structures and that these structures have widespread regulatory functions.