The evaluation of metabolomics data sets involves multiples steps of data processing, statistical analysis and interpretation. XCMS is a commonly employed program for analyzing metabolomics data. It exists in two distinct variants: XCMS/R and XCMS Online. XCMS/R is a package for the statistics and graphics language R which requires manual coding, allowing for highly customized workflows. In contrast, XCMS Online provides a user-friendly web interface with modules for statistics and metabolic pathway integration. We demonstrate the step-by-step use of both platforms through the analysis of a liquid-chromatography/high-resolution mass spectrometry dataset of flowers of Arabidopsis thaliana (accessions Col and Ws). Both workflows identify common features in the twelve samples (2 accessions × 6 biological replicates). However, the general purpose of the programs is different. XCMS/R is more focused on optimizing the parameter settings and statistical testing/visualization. In contrast, XCMS Online performs most of the tasks automatically and supports the mapping of results on biochemical pathways.