There is a growing need for understanding the exposome chemical space. Non-target analysis is, generally, used for the analysis of the thousand of known and unknown chemicals in environmentally and biologically relevant samples. However, algorithm limitations arise with regard to flexibility and suitability for the processing of such data. Hence, the modular open-access and open-source jHRMS toolbox was developed, providing both a user-interface and the freedom to modify and add workflows as required. The default implemented algorithms have been developed for high-resolution mass spectrometry data and can handle MS1 and various data-dependent and data-independent analysis data types both in profile and centroided formats. Moreover, the identification algorithm provides extensive match quality reporting. Besides the data processing workflow, the toolbox comes with built in post processing (i.e., visualization) for individual steps of the workflow and statistical analysis. Finally, the results are reported step-by-step, parameters can be saved, and it is operating system agnostic. To showcase the potential of the jHRMS toolbox, two datasets from different origins environmental and biological were analyzed and reported. For the environmental case study the trends of some pharmaceuticals in river waters were evaluated. While for the biological samples it was possible to differentiate between liver and brain tissues based on the extracted information.