Invasive species are anticipated to emerge in the future with equal or even higher rates than those recorded in the past. Plant pest emergence has serious negative environmental, economic, and social implications. The European Food Safety Authority was requested to develop a methodology for scoring the identified pests that may be eligible to be assessed as a potential threat. The methodology that was developed, PeMoScoring, consists in a list of criteria/questions to be answered choosing among pre-set scores. The result feeds a multi-criteria analysis that, by pairwise comparison with a set of reference pests, allows concluding whether the pest under evaluation provides sufficient evidence to be considered a threat (positive PeMo) or not (negative PeMo). In this article, PeMoScoring is described by using practical examples of four insects that have been previously evaluated: Arboridia kakogawana, Phenacoccus solenopsis, Adelges tsugae and Singhiella simplex. The PeMoScoring results, which were positive for the first two and negative for the last two pests respectively, are compared in terms of the information leading to the specific outcome. Overall, PeMoScoring proves to be a practical tool that can generate fast and reproducible results. Given its plasticity for prioritising pests in the context of risk analysis of emerging threats, accessibility should be granted before long to potential users within and outside the field of plant health.