This study aims to evaluate opportunities to use the online classification system BioClass for phytosanitary risk assessment. BioClass is a GIS tool designed to solve multiple-criteria classification and optimization problems. The aim of BioClass is to introduce advances in Multi-objective Decision Making for real world problems. In BioClass we joined the advantages of rough sets, crisp level sets and fuzzy sets methods to improve classification processes. Information from pest models can be used to simulate and predict the intensity and potential pest threat. Interactions among microclimate components on sawfly (Haplocampa testudinea), codling moth (Cydia pomonella L.) and scab (Venturia inaequalis) using GIS technologies was studied. For modeling, maps of the sum of active and effective temperatures were constructed by the Kriging interpolation method. The precision of beginning of the continuous flight of apple coddling moth and the calendar date for the first and second treatment in the orchards with a high and medium density of the pest were calculated. The accuracy of the forecast model for different sectors was 1–3 days. The BioClass system was used to identify pest economic damage thresholds in space for the identification of outbreaks and application of protective measures with the help of small flying devices of the drone type. The results confirmed that the BioClass classification system can be used for the online agro-ecological classification of the territory at household, region, country level and to provide farmers' consultation centers and forecasting stations with precise information for phytosanitary risk assessment.