Species distribution models (SDMs) are widely used in ecology and conservation. However, their performance is known to be affected by a variety of factors related to species occurrence characteristics. In this study, we used a virtual species approach to overcome the difficulties associated with testing of combined effects of those factors on performance of presence-only SDMs when using real data. We focused on the individual and combined roles of factors related to response variable (i.e. sample size, sampling bias, environmental filtering, species prevalence, and species response to environmental gradients). Results suggest that environmental filtering is not necessarily helpful and should not be performed blindly, without evidence of bias in species occurrences. The more gradual the species response to environmental gradients is, the greater is the model sensitivity to an inappropriate use of environmental filtering, although this sensitivity decreases with higher species prevalence. Results show that SDMs are affected to the greatest degree by the species response to environmental gradients, species prevalence, and sample size. Models’ accuracy decreased with sample size below 300 presences. Furthermore, a high level of interactions among individual factors was observed. Ignoring the combined effects of factors may lead to misleading outcomes and conclusions.