No two cells are exactly alike, not even when they share the same genome and live in the same environment. Intracellular processes generate variation between cells at multiple levels, from shifts in physiological states to stress responses and mutagenesis. I will first discuss our work on the phenotypic heterogeneity of Escherichia coli, showing how the accumulation of damaged proteins within individual cells drives changes in gene expression, growth, and the inheritance of cellular components. I will then turn to my current work on the emergence of genetic variation, where we investigate how transcriptional pausing and its interplay with DNA repair pathways can promote mutagenesis in unstressed cells. Together, these studies ask how processes occurring within individual cells shape the diversity of bacterial populations.