Given the current urbanization context and rising interest in green roof systems, growing a high-value crop such as saffron crocus in green roof medium could be an opportunity to use the benefits of both the crop and the green roof system; the drainage, aeration, and sand-like texture of green roof media make it suited for saffron production, and the saffron market price could make green roof production commercially viable. Various factors, including plant diseases and planting depth, could affect saffron production. Therefore, this research was conducted to evaluate the effects of planting depth and biofungicide treatments using Bacillus subtilis on saffron production in a green roof system. A completely randomized factorial block design was used with planting depth (10 cm and 15 cm) and B. subtilis strain QST 713 biofungicide treatments (an untreated control, 15.6 × 109 cfu/L, and 31.2 × 109 cfu/L) as independent variables. In 2019, fresh flower yield, fresh stigma yield, and dry stigma yield were calculated during harvesting, and additional data on flower number, tepal length and width, stigma length, and harvest time were collected in 2020. All variables were analyzed using analysis of variance (ANOVA) with planting depth and biofungicide treatments as fixed effects using R. Fresh stigma yield and dry stigma yield were higher in the 10-cm planting depth in 2019. Results were opposite in 2020: flower number, fresh flower yield, fresh stigma yield, dry stigma yield, and harvest time were higher in the 15-cm planting depth than the 10-cm planting depth. B. subtilis treatments did not affect any studied variable in 2020, but in 2019, the higher level of fungicide treatment resulted in lower fresh flower yield and dry stigma yield. There was no effect of biofungicide treatment and planting depth on tepal length, tepal width, and stigma length in both years. This study showed that growing saffron crocus on green roofs is feasible and even resulted in higher yield than field production in many saffron-producing regions and countries. In addition, results indicated that shallow planting might be suitable for annual production, whereas deeper planting could be ideal for perennial production based on the objective. Our findings demonstrated the feasibility of saffron production in the green roof system and suggest further research to develop best management practices.