Cultivar may be an important factor associated with the occurrence and severity of sooty blotch and flyspeck (SBFS) fungi in apple. The aim of the study was to analyse the influence of 28 cultivar features on the occurrence of the SBFS complex in apple and to categorize the importance of each using a multivariate approach. Features were classified as agronomic (related to fruiting and growing behaviour and to susceptibility to other diseases; 11 features), morphological (describing fruit morphology; 11) and technological (related to the chemical composition of the fruit juice; 6). Susceptibility to SBFS varied widely among cultivars. The predictive value of some features was not the same for the signs of SB and FS, possibly because each sign is produced by a different species complex which may behave differentially against environmental variables, including the cultivar. Our results showed that agronomic features as a whole were more significant than morphological or technological ones for explaining the cultivar variability in damage. Those related to fruit development phenology were the more explanatory among the agronomic features: late-maturing cultivars suffered higher damage. The intensity of colour was the most explanatory variable among the features describing fruit morphology, showing that SBFS severity was greater on light-coloured apples. Russeting level or skin texture, amongst other variables, were significant but less predictive. The technological features were least explanatory: FS damage was favoured by lower sugar content and higher phenol content at harvest, whereas variability in SB signs was not explained by any juice parameter. The multivariate approach allowed us to select the most important variables in relation to SBFS damage and to discard those without influence, which may be a valuable contribution to understand SBFS development. This research highlights the need of a proper choice of cultivar to reduce disease severity.