Cold plasma technology is gaining attention as a promising approach to enhancing the bioactivity of plant extracts. However, its impact on green coffee bean extracts (GCBEs) still needs to be explored. In this study, an innovative underwater plasma jet system was employed to investigate the effects of cold plasma on Coffea arabica GCBEs, focusing on the conjugation reflected by the change in composition and bioactivity. The DPPH radical scavenging antioxidant activity exhibited a gradual increase with plasma treatment up to 35 min, followed by a decline. Remarkably, at 35 min, the plasma treatment resulted in a significant 66% increase in the DPPH radical scavenging activity of the GCBE. The total phenolic compound content also displayed a similar increasing trend to the DPPH radical scavenging activity. However, the phenolic profile analysis indicated a significant decrease in chlorogenic acids and caffeine. Furthermore, the chemical composition analysis revealed a decrease in free amino acids, while sucrose remained unchanged. Additionally, the SDS-PAGE results suggested a slight increase in protein size. The observed enhancement in antioxidant activity, despite the reduction in the two major antioxidants in the GCBE, along with the increase in protein size, might suggest the occurrence of conjugation processes induced by plasma, particularly involving proteins and phenolic compounds. Notably, the plasma treatment exhibited no adverse effects on the extract’s safety, as confirmed by the MTT assay. These findings indicate that cold plasma treatment holds significant promise in improving the functional properties of GCBE while ensuring its safety. Incorporating cold plasma technology into the processing of natural extracts may offer exciting opportunities for developing novel and potent antioxidant-rich products.