Ethidium bromide–acridine orange (EB/AO) is one of the fastest, most economically valid methods for separating living and dead cells in plant root tips. The present study aimed to investigate the apoptotic effect, nuclear abnormalities and cell division index using an Allium cepa test assay with EB/AO staining and an ImageJ program. Nickel sulphate (NiSO4) concentrations (1.75, 3.5, 7 and 14 ppm) were exposed to the root germination of A. cepa for 48 and 72 h to observe mitotic abnormalities, cytotoxic effects and 5-day exposure to apoptotic effects. It was found that amorphous nuclei, vacuolisation and C-mitosis were the most observed abnormalities, which increased at 14 ppm NiSO4 exposure after 48 and 72 h. The total number of nuclear abnormalities significantly increased at all concentrations and exposure periods. The ImageJ program was used to determine apoptosis rates. The data obtained showed that high concentrations of NiSO4 caused significantly more cell death in root tips than in the control group, resulting in root growth inhibition and increased apoptosis with increased concentration and exposure period. NiSO4 caused toxic activity on root growth, identified as apoptosis, especially at the cortex and vascular region in the root tips. The study found affected damaged and apoptotic areas on the root tips using an EB/AO staining method, which can be used as a marker of damaged tissue areas.