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 carried out in 2021 at the Seed Research Laboratory, Research Greenhouse, and Plant Disease Laboratory, Faculty of Agriculture, 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) 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 of treatments in laboratory conditions showed that the lowest germination percentage, mean germination time and allometric coefficient were obtained from 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, prolonged mean germination time, reduced germination rate coefficient, and 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 diameter of the fungal colony on the third and sixth day was obtained from the 2% concentration of extract, which had no statistically significant difference with the 1% concentration of 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, considering the results of this study and conducting more research in the field of fungicidal and allotoxic effects of saffron organ extracts, it is possible to produce natural fungicides and herbicides.