This study proposes a new workflow for crop growth evaluation and yield calibration in the Soil and Water Assessment Tool Plus (SWAT+) model and evaluates its impact on simulated hydrological and biogeochemical processes. The workflow was applied for ten small agricultural catchments in Europe. A detailed demonstration is provided for the German catchment, Schwarzer Schöps. The workflow proved effective across all catchments, improving yield calibration from an initial R2 of 0.5–0.84. The results show that evapotranspiration and soil moisture were only moderately affected by crop calibration in three catchments (Belgium, Czech Republic and Norway) and negligibly changed in the remaining ones. Sediment and nutrient balance were affected more strongly: sediment, nitrogen and phosphorus loss change reached 82 % (Norway), 16 % and 20 % (Czech Republic), respectively. The proposed workflow is a valuable tool for improving the accuracy of SWAT + simulations and can be used to support decision-making in environmental management.