Recent advancements in single-cell omics technologies have significantly enhanced our ability to analyze individual microbial cells at the genomic, transcriptomic, and metabolomic levels. While single-cell analysis has traditionally focused on eukaryotic systems, emerging methodologies now enable high-throughput studies of environmental microbiomes and viruses, providing deeper insights into microbial ecology and functional diversity. Microfluidic droplet-based single-cell genomics has improved whole-genome amplification efficiency while minimizing contamination, enabling the sequencing of thousands of microbial genomes with higher accuracy. Targeted single-cell genomics techniques have further refined genome recovery by selectively isolating cells containing specific genetic sequences. These innovations have advanced our understanding of microbial community structures and host-microbe interactions. Single-cell transcriptomics have revealed substantial gene expression variability within bacterial populations, highlighting mechanisms of stress adaptation, antibiotic resistance, and virulence. Despite technical challenges, including the lack of poly-A tails and low RNA content, recent breakthroughs in scRNA-seq methodologies have improved sensitivity and throughput, enabling high-resolution transcriptional profiling. Single-cell metabolomics, particularly through Raman microspectroscopy, offers label-free, nondestructive metabolic profiling at subcellular resolution. Integration with computational tools such as multivariate curve resolution (MCR) analysis has facilitated the identification of metabolic heterogeneity and cellular differentiation processes. These approaches are increasingly being applied to biotechnology, environmental microbiology, and biomedical research. Future advancements in single-cell omics, including multi-omics integration and AI-driven data analysis, will further enhance our understanding of microbial functions and interactions. These technologies hold promises for diverse applications, from microbial ecology to biomanufacturing, by enabling unprecedented insights into the molecular mechanisms that govern microbial life.