There is growing interest and appreciation in the use of mass spectrometry-based multi-omics approaches to study biological processes and diseases from a systems-level perspective. The performance of discovery-level multi-omics typically involves the partitioning of a complex sample in its individual components, followed by thorough analysis of each “ome” under optimized LC and MS conditions. However, these multi-omics experiments must be streamlined before their findings can be implemented into diagnostic or prognostic applications. The rapid gas-phase structural separations afforded by IM-MS provides an opportunity for high-throughput measurements of biological samples containing mixtures of lipids, metabolites, peptides, and other biochemicals. We are developing methods for single injection high-throughput multi-omics based on flow injection analysis (FI) and ion mobility-mass spectrometry (IM-MS). The feasibility and advantages of FI-IM-MS will be demonstrated for the identification of microorganisms to the species and strain levels using integrated lipidomic and metabolomic features.