Mineral fertilizers are a source of nutrients for crops, but their excessive use can have devastating effects on the environment. The aim of this study was to investigate the effect of granulated organic phosphate fertilizer on the germination rate, cell proliferation, and nucleolus morphology in root meristem cells of edible onion seeds (Allium cepa L.). To this aim, onion seeds were cultured in plates containing distilled water (control) or fertilizer solutionat two doses (0.089 and 0.177 g) for 72 hours. Subsequently, mitotic and phase indices, frequency of mitotic abnormalities, nuclear and nucleolar area, and number of nucleoli in root tip meristem cells were evaluated. The concentrations of lead, nickel, cadmium, and copper in the fertilizer solution was also measured which were 0.451, 0.120, 0.040, and 0.002 mg/L respectively. To examine differences between the studied groups in terms of the evaluated indices, the Kruskal-Wallis and Jonckheer-Trepstra test was used. According to the results, no significant differences were observed among the three groups for the indices mentioned above. However, the average germination percentage and anaphase index decreased with increasing fertilizer concentration, and this trend was statistically significant (Germination percentage: p=0.045, TJT=4.5; Anaphase index: p=0.020, TJT=3.00). The results of this study showed that the use of this fertilizer can reduce the germination rate of onion seeds and anaphase index during cell division in root tip meristem cells of this plant. Further studies are required to better understand the harmful biological effects of chemical fertilizers.