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There is a strong need to develop eco-sustainable agricultural techniques to improve crop yields while preserving biomolecule contents and reducing the adverse environmental impact of agro-chemicals. The use of microorganisms in agriculture represents an attractive and innovative solution. Herein, a chemical study on the nutritional and sensory qualities of San Marzano Cirio 3 (SMC3), Corbarino (CO) and Brandywine (BW) tomato varieties cultivated with and without effective microorganisms (EM) is reported. LC–MS analysis of the methanolic extracts allowed for the identification of 21 polyphenol derivatives. In different proportions among the studied varieties, the two main polyphenols were rutin and naringenin chalcone; the latter was isolated and chemically identified by complementary HR-ESIMS/MS and NMR methods. SMC3 and CO were richer in naringenin chalcone. Conversely, BW showed higher proportions of rutin; however, in all cases, the relative amounts of the two polyphenols considered together increased over the other minor components after the EM treatment. The qualitative and quantitative HPLC analyses of taste-active compounds (aspartic acid, glutamic acid, AMP and GMP) revealed a significant difference in aspartic and glutamic acids and ribonucleotide contents according to the cultivation condition (±EM), particularly in BW. This study provides chemical data in support of the use of EM green technology for the cultivation of edible agricultural products, such as tomato preserves, and may even improve nutritional and sensory qualities while safeguarding the environment.