Omics technologies, aka genomics, transcriptomics, proteomics, and metabolomics are powerful tools to elucidate microbial and functional dark matter. Single-cell technologies have aided in the understanding of heterogeneity and phenotypic differences of and between cells in microbial communities, enabling new insights into diversity, evolutionary histories, metabolic pathways, and potentials for biotechnological applications. Nevertheless, to fully understand single-cell biology in a complete and comprehensive way, multiple ‘omics technologies have to be combined and applied simultaneously to one individual cell. Single-cell multi-omics methods have been used in eukaryotes for the last ten years; however, they still face challenges and limitations for applications in prokaryotes. In this chapter, we describe state-of-the-art technologies and future perspectives for the use of single-cell multi-omics in bacteria and archaea.