Extraction of meaningful biological information from the vast array of data that metabolomics analyses generate is a major challenge in the field. A variety of computational and visual tools that help to identify changes in metabolic pathways have been proposed including functional analysis and pathway analysis. Meta-analysis of metabolomic data has emerged as a powerful source of information. In this work, the applicability of the Mantel's test for the correlation of functional results from metabolic pathway analysis is shown using experimental and simulated data sets as evaluation examples. The statistical significance of the correlation coefficient can be assessed by permutation testing requiring practically no computation time. The use of the Mantel's test can assist the critical comparison of different phenotypes, studies, methods, platforms, or data preprocessing strategies, as well as help to identify inconsistencies between metabolomic study outcomes, making this algorithm attractive for data interpretation and meta-analysis on a routine basis. Display omitted •The Mantel's test enables the correlation of metabolic pathway analysis results.•The test can be used for the critical evaluation of different metabolomic studies.•The test is well established, and it requires practically no computation time.