In the present study, a new method for a decision-support system for fungicide administration against the pathogen Botrytis cinerea in vineyards was developed based on Integrated Pest Management principles which identified an infection risk before the appearance of disease symptoms. The proposed method is based on the combination of (i) the phenological observations of the main susceptible stages to infection, (ii) the airborne spores monitoring, (iii) the forecasting of the suitable meteorological conditions for B. cinerea spore germination during the subsequent 4–6 days after the spore detection. Aerobiological, phenological and meteorological analyses were carried out using data from 2008 to 2015 in a vineyard of Northwestern Spain. Aerobiological spore data were obtained using a Lanzoni VPPS-2000 pollen-spore trap. Phenological observations were conducted on 22 plants of Treixadura cultivar following the BBCH (Biologische Bundesanstalt für Land und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scale. The Magarey generic fungal model was applied for the identification of the main meteorological suitable periods for infection within the susceptible phenological stages of flowering and ripening of berries. Our results showed that climatic conditions favoured fungal development during flowering, although a higher incidence of B. cinerea infection risk-periods occurred during the prior-to-harvest stage of ripening of berries, the most susceptible phenological stage to B. cinerea infection obtained by the proposed methodology. This approach enables more precise targeting in pesticide spraying and reduction in pesticide application from 4–5 to 2–3 times per year at our commercial study. It also illustrates the real-world benefits of integrated disease risk modelling.