© 2014 John Wiley & Sons, Inc. This chapter examines new developments in imaging that further advance our ability to see into microbial forms and functions. It focuses on the more recent application of imaging mass spectrometry (IMS) to bacterial metabolism. The chapter briefly describes the IMS methods most commonly used in microbiology. It discusses the applications of IMS to bacterial ecology and primary metabolism to illustrate differences in resolution and versatility of the methods. The chapter further addresses examples where IMS has been applied to secondary metabolism, biosynthesis of natural products, and bacterial interactions mediated by these metabolites. IMS integrates well with the existing toolbox for imaging and metabolic studies in microbial ecology. Two common methodologies are fluorescence in situ hybridization (FISH) for the identification of organisms and stable isotope probing (SIP) for monitoring nutrient fluxes. Finally, the chapter highlights recent advances that point to a promising future for IMS in microbiology and natural product research.