Copper-based materials are actively explored for their potential as antimicrobial agents. However, recent studies show that sublethal concentrations of Cu ions can induce the viable-but-non-culturable (VBNC) cell state in certain bacteria, hampering with contamination control and monitoring. Despite the growing number of omics studies investigating the VBNC state, the underlying molecular mechanisms remain largely enigmatic. Here, we determine variations in protein expression of Cupriavidus metallidurans CH34 in different phases of the Cu-induced VBNC state via quantitative LC-MS/MS analysis at multiple sample time points. With this approach, we aimed to reveal cellular adaptations triggering VBNC formation and the characteristic spontaneous recovery of culturability (resuscitation). This submission contains controls and is part of the other pride submission PXD056297.