Fungal pathogens and especially grey mould are among the most virulent bio-aggressors of protected crops. A warm, moist greenhouse climate encourages the outbreak of explosive epidemics, of Botrytis cinerea in particular. The aim of this study was to simulate Botrytis spore concentration and deposition patterns in a greenhouse and model the inside climate conditions. The general flow equations were solved using the Fluent® CFD code with a simulation of the coupling between aerial transport and crop activity based on earlier research. A specific Eulerian particle transfer module was added to account for spore transfer with a new species: the Botrytis spore concentration. To describe the spore transport equation, the governing equations were modified, adding a vertical terminal velocity term accounting for the effect of gravity on the spores and sink terms accounting for spore interception by impaction or deposition. The necessary parameters for the model, together with spore concentration and climate boundary conditions, were determined in an experimental study of a rose greenhouse with roof and lateral vents equipped with insect-proof nets. These experimental devices have already been exploited for validating a ventilation model and a Botrytis spore balance. In addition to these previous studies, the present paper was essentially designed to determine greenhouse climate and spore concentration and deposition patterns. The accuracy of the inside–outside air temperature difference simulation is good but deteriorates for inside–outside air humidity. Spore transfer is also accurately simulated, with a mean error of only 0.2 sp m−3 for daytime and 0.53 sp m−3 for night time. The observed values of spore deposition show a similar order of magnitude to the simulations. However, validation was hindered by difficulties encountered in measuring spore deposition, even on an average daily time scale. Analysis of the heterogeneity of the simulated distribution of spore deposition and concentration revealed that, when the Botrytis spores came from outside, their concentrations in the air are filtered by the insect proof nets on the vent openings and then by the crop canopy – the rose stems, buds and leaves. Consequently, if, as in this case, no inoculums is produced inside the greenhouse, we note a considerable decrease in inside airborne spore concentration due to these various filters and considerable spore deposition on the crop cover near the vent openings where the air enters. This approach can provide information's on the patterns of inoculums deposition and climate conditions explaining the risks of future fungal development.