Exploring the metabolic differences directly on tissues is essential for the comprehensive understanding of how multicellular organisms function. Mass spectrometry imaging (MSI) is an attractive technique toward this goal; however, MSI in metabolomics scale has been hindered by multiple limitations. This is most notable for single cell level high-spatial resolution imaging because of the limited number of molecules in small sampling size and the low ionization yields of many metabolites. Several on-tissue chemical derivatization approaches have been reported to increase MSI signals of targeted compounds, especially in matrix-assisted laser desorption/ionization (MALDI)- MSI. Herein, we adopt a combination of chemical derivatization reactions, to selectively enhance metabolite signals of a specific functional group for each consecutive tissue section. Three well-known on-tissue derivatization methods were used as a proof of concept experiment: coniferyl aldehyde for primary amines, Girard’s reagent T for carbonyl groups, and 2-picolylamine for carboxylic acids. This strategy was applied to the cross-sections of leaves and roots from two different maize genotypes (B73 and Mo17), and enabled the detection of over six hundred new unique metabolite features compared to without modification. Statistical analysis indicated quantitative variation between metabolites in the tissue sections, while MS images revealed differences in localization of these metabolites. Combined, this untargeted approach facilitated the visualization of various classes of compounds, demonstrating the potential for untargeted MSI in the metabolomics scale.