Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailoredand straightforwardnon-target analysis workflows. This platform makes the usage, evaluation and mixing of well-tested algorithms seamless by harmonizing various commonly (primarily open) software tools under a consistent interface. In addition, patRoonoffersvarious functionality and strategies tosimplify and perform automated processing of complex (environmental) data effectively.patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform a straightforward and effective non-target analysis was demonstrated with real-world environmental samples, showing thatpatRoonmakes comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.