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Simple Summary: Cold atmospheric plasma (CAP) and plasma-activated medium (PAM) are known to selectively kill cancer cells, however the efficacy of CAP in cancer cells following epithelial-mesenchymal transition (EMT), a process which endows cancer cells with increased stemness, metastatic potential, and resistance to conventional therapies, has not been previously examined. We have used several established models of EMT to show that PAM is significantly more active in cancer cells exhibiting EMT than their epithelial counterparts. We further show that this enhancement correlated with increased levels of reactive oxygen species (ROS) in the mesenchymally-shifted cell lines. Cold atmospheric plasma (CAP) has emerged as a highly selective anticancer agent, most recently in the form of plasma-activated medium (PAM). Since epithelial–mesenchymal transition (EMT) has been implicated in resistance to various cancer therapies, we assessed whether EMT status is associated with PAM response. Mesenchymal breast cancer cell lines, as well as the mesenchymal variant in an isogenic EMT/MET human breast cancer cell system (PMC42-ET/LA), were more sensitive to PAM treatment than their epithelial counterparts, contrary to their responses to other therapies. The same trend was seen in luminal muscle-invasive bladder cancer model (TSU-Pr1/B1/B2) and the non-muscle-invasive basal 5637 bladder cancer cell line. Three-dimensional spheroid cultures of the bladder cancer cell lines were less sensitive to the PAM treatment compared to their two-dimensional counterparts; however, incrementally better responses were again seen in more mesenchymally-shifted cell lines. This study provides evidence that PAM preferentially inhibits mesenchymally-shifted carcinoma cells, which have been associated with resistance to other therapies. Thus, PAM may represent a novel treatment that can selectively inhibit triple-negative breast cancers and a subset of aggressive bladder cancers, which tend to be more mesenchymal. Our approach may potentially be utilized for other aggressive cancers exhibiting EMT and opens new opportunities for CAP and PAM as a promising new onco-therapy. [ABSTRACT FROM AUTHOR]