To evaluate the allelopathic and antifungal effects of saffron (Crocus sativus L.) leaf and corm extracts on the germination and early growth of Peganum harmala and on the mycelial growth of Fusarium nygamai, three independent factorial experiments were conducted using a completely randomized design with three replications. The experiments were conducted in 2021 at the Seed Research Laboratory, Research Greenhouse, and Plant Disease Laboratory of the Faculty of Agriculture at the University of Birjand. In the first experiment (laboratory bioassay), treatments consisted of two saffron plant organs (leaf and corm) and seven extract concentrations (0, 0.0625, 0.125, 0.25, 0.5, 1, and 2% w.v^-1) applied to assess inhibitory effects on the germination parameters of wild rue seeds. The second experiment (greenhouse pot study) employed identical treatments to evaluate seedling emergence and growth characteristics. In the third experiment, the same treatment structure was used to investigate the inhibitory effects of extracts on the mycelial growth of F. nygamai. The results of the interaction between treatments under laboratory conditions showed that the lowest germination percentage, mean germination time, and allometric coefficient were obtained with the 2% concentration of corm extract. The lowest length of radicle and shoot, dry weight of shoot, and root were obtained from the 2% concentration of corm extract. In greenhouse conditions, the 2% corm extract and the 1 and 2% leaf extract treatments resulted in the lowest germination percentage, the longest mean germination time, the lowest germination rate coefficient, and the lowest allometric coefficient. Furthermore, the minimum shoot length, root length, shoot dry weight, and root fresh weight were obtained from the same treatments. The results of the antifungal test showed that the lowest colony diameter on the third and sixth days was observed with the 2% extract, which did not differ significantly from that of the 1% extract. On the ninth day, the lowest colony diameter was obtained from a concentration of 2% corm extract, which had no statistically significant difference with concentrations of 1 and 2% leaf extract. Finally, the results of these experiments showed that the effect of inhibiting germination and growth of wild rue in laboratory conditions was greater in saffron corm extract and in greenhouse conditions in leaf extract, and the antifungal effect of leaf extract was greater. Therefore, based on the results of this study and further research into the fungicidal and allotoxic effects of saffron organ extracts, it is possible to develop natural fungicides and herbicides.