Despite the proposal of minimum reporting guidelines for metabolomics over a decade ago, reporting on the data analysis step in metabolomics has been shown to be unclear and incomplete with major omissions and lack of logical flow rendering the data analysis’ workflows in these studies impossible to follow and therefore replicate or even imitate. Here we propose possible reasons why the original guidelines have had poor adherence and present an approach to improve their uptake. We present in this paper an R markdown reporting template file that guides the production of text and generates workflow diagrams based on user input. This R Markdown template contains, as an example in this instance, a set of minimum information requirements specifically for the data pre-treatment and data analysis section of biomarker discovery metabolomics studies, (gleaned directly from the original proposed guidelines by Goodacre at al.). These minimum requirements are presented in the format of a questionnaire checklist in an R markdown template file. The R Markdown reporting template proposed here can be presented as a starting point to encourage the data analysis section of a metabolomics manuscript to have a more logical and stepwise presentation and to contain enough information to be understandable and reusable. The idea is that these guidelines would open to user feedback, modification and updating by the metabolomics community via GitHub.