The need for sustainable agriculture amid a growing population and challenging climatic conditions is hindered by the environmental repercussions of widespread fertilizer use, resulting in the accumulation of metal ions and the loss of micronutrients. The present study provides an approach to improve the efficiency of nanofertilizers by controlling the release of copper (Cu) ions from copper oxide (CuO) nanofertilizers through bioionic liquids based on plant growth regulators (PGR-ILs). A 7-day study was conducted to understand the kinetics of Cu ion release in aqueous solution of five different PGR-ILs, with choline ascorbate ([Cho][Asc]) or choline salicylate ([Cho][Sal]) leading to 200- to 700-fold higher dissolution of Cu ions in comparison to choline indole-3-acetate ([Cho][IAA]), choline indole-3-butyrate ([Cho][IBA]), and choline gibberellate ([Cho][GA3]). The tunable diffusion of Cu ions from CuO nanofertilizers using PGR-ILs is then applied in a foliar spray study, evaluating its impact on the growth phenotype, photosynthetic parameters, and carbon dioxide (CO2) sequestration in Nicotiana tabacum in a greenhouse. The results indicate that nanoformulations with lower concentrations of Cu ions in PGR-IL solutions exhibit superior outcomes in terms of plant length, net photosynthetic rate, dry biomass yield, and CO2 sequestration, emphasizing the critical role of dissolution kinetics in determining the effectiveness of PGR-IL-based nanoformulations for sustainable agriculture.