To uncover metal toxicity targets and defense mechanisms of the facultative anaerobe Pantoea strain sp. MT58 (MT58), we used a multi-omic strategy combining two global techniques, random bar code transposon-site sequencing (RB-TnSeq) and activity-based metabolomics. MT58 is a metal-tolerant Oak Ridge Reservation (ORR) environmental isolate that was enriched in the presence of metals at concentrations measured in contaminated groundwater at an ORR nuclear waste site. The effects of three chemically-different metals found at elevated concentrations in the ORR contaminated environment were investigated: the cation Al3+, the oxyanion CrO42-, and the oxycation UO22+. Both global techniques were applied using all three metals under both aerobic and anaerobic cultures to elucidate metal interactions mediated through the activity of metabolites and key genes/proteins. These revealed that Al3+ binds intracellular arginine, CrO42- enters the cell through sulfate transporters and oxidizes intracellular reduced thiols, and membrane-bound lipopolysaccharides protect the cell from UO22+ toxicity. In addition, the Tol outer membrane system contributed to the protection of cellular integrity from the toxic effects of all three metals. Likewise, we found evidence of regulation of lipid content in membranes under metal stress. Individually, RB-TnSeq and metabolomics are powerful tools to explore the impact various stresses have on biological systems. Herein we show that together they can be used synergistically to identify the molecular actors and mechanisms of these pertubations to an organism furthering our understanding of how living systems interact with their environment. Importance Studying microbial interactions with their environment can lead to a deeper understanding of biological molecular mechanisms. In this manuscript, two global techniques, RB-TnSeq and activity metabolomics, were successfully used to probe the interactions between a metal resistant microorganism, Pantoea strain sp. MT58, and metals contaminating a site where the organism can be located. A number of novel metal to microbe interactions were uncovered including Al3+ toxicity targeting arginine synthesis, which could lead to a deeper understanding of the impact Al3+ contamination has on microbial communities as well as its impact on higher level organisms including plants for whom Al3+ contamination is an issue. Using multi-omic approaches as the one described here is a way to further our understanding of microbial interactions and their impacts on the environment overall.