Floods and droughts are the events that most threaten crop production; however, the impact of floods on crops is still not fully understood and often under-reported. Nowadays, multiple sources of information and approaches support the estimation of agricultural losses due to floods. This study aims to understand the differences in agricultural loss estimates provided by two conceptually different approaches (crop models and expert-based models), evaluating their sensitivity to flood hazard inputs. We investigated the challenges in flood agricultural loss assessments referring to a case study for which, in addition to model simulations, information from surveys and on-site inspections were available. Two crop models (APSIM and WOFOST) and the expert-based model AGRIDE-c were applied to evaluate agricultural yield losses after the flood event of the Panaro River (Emilia-Romagna, Northern Italy) that took place on the 6 December 2020. Two modelling tools were used to reproduce the event: the hydraulic model HEC-RAS and the image-based tool FwDET. Additionally, surveys among local farmers were conducted in the aftermath of the event to evaluate the flood features (water depth, extent and duration) and crop losses. The main findings of the study are that APSIM and WOFOST provide similar estimates of yield losses, while AGRIDE-c tends to underestimate yield losses when the losses over the entire study area are evaluated. The choice of the flood simulation technique does not influence the loss estimation since the difference between the yield loss estimates retrieved from the same model initialized with HEC-RAS or FwDET was always lower than 2%. Information retrieved from the surveys was not sufficient to validate the damage estimates provided by the models but could be used to derive a qualitative picture of the event. Therefore, further research is needed to understand how to effectively incorporate this kind of information in agricultural loss estimation.