The term ‘clustered regularly interspaced short palindromic repeats’ (CRISPR) has recently become synonymous with the genome-editing revolution. The RNA-guided endonuclease CRISPR-associated protein 9 (Cas9), in particular, has attracted attention for its promise in basic research and gene editing-based therapeutics. CRISPR-Cas systems are efficient and easily programmable nucleic acid-targeting tools, with uses reaching beyond research and therapeutic development into the precision breeding of plants and animals and the engineering of industrial microbes. CRISPR-Cas systems have potential for many microbial engineering applications, including bacterial strain typing, immunization of cultures, autoimmunity or self-targeted cell killing, and the engineering or control of metabolic pathways for improved biochemical synthesis. In this review, we explore the fundamental characteristics of CRISPR-Cas systems and highlight how these features can be used in industrial settings. CRISPR-Cas systems have enabled genome editing in multiple industrially relevant species and provided genetic tools that were previously unavailable. Editing requires only two components (a Cas nuclease and a programmable guide RNA), requires minimal technical expertise to implement, and can be multiplexed for simultaneous modification of multiple sites in a single transformation event. CRISPR-Cas systems can be used to edit a genome through gene knockouts or homology-mediated knockins to control transcription of exogenous or endogenous genes, and to serve as an antimicrobial or antiviral immunization system. CRISPR-Cas-mediated engineering can increase the number of chemicals and products that are accessible through fermentation and broaden the diversity of strains suitable for industrial production.