With the ever-increasing demand for improved medical diagnosis, safe food supply, advanced biotechnology, and sustainable ecosystems, characterization of the microbial world by sensitive, specific, rapid, and quantitative tools is gaining more and more attentions. Surface-enhanced Raman spectroscopy (SERS) and its flexible integration with other tools, such as microscopes, stable isotope probing, microfluidic analysis, and chemometric analysis, have advanced rapidly and showed great promise for versatile microbial characterization. This perspective provides an overview of the recent advances of SERS and related coupling techniques for microbial diagnosis (e.g., identification and antibiotic resistance testing), phenotypic response profiling, microbial function assessment, in situ biofilm characterization, and multifunctional SERS tags. We further propose future requirements and the direction for SERS methodology to be headed, including standardization of SERS methodology, database generation and management, coupling with omics technology and single-cell sorting, and application in deciphering microbial processes.