Banana (Musa) is one of the most important economic and staple crops in the world. The majority of edible cultivated banana species arises from two species of the Eumusa group, Musa acuminata (A genome) and Musa balbisiana(B genome). In order to assess the biochemical diversity that exists in our banana germplasm collections multi-platform metabolomics platforms has been established for banana. These include LC-MS in untargeted and targeted mode, GC-MS based metabolite profiling and targeted UPLC-PDA for compounds such as carotenoids where MS ionisation is poor. Metabolomic finger printing and complementary targeted analysis has been performed on in vitro vegetative material for 20 diverse Musa accessions, including diploid varieties, wild Musa acuminata and Musa balbisiana as well as different triploids and distant wild species (Musa ornata). The data allowed the separation of the genotypes on the basis of genotypes and differentiating metabolites identified between accessions. Comparisons with field grown material was carried out in selected cases and clear correlation was observed including the potential to predict fruit phenotypes on vegetative profiles. These robust techniques can now be utilised in combination with of omic approaches to characterise consumer and agronomic traits within breeding populations.