Background: Eggplant (Solanum melongena L.) is rich in health-promoting phenolic acids, primarily in the chlorogenic acid. For the production of chlorogenic acid in the eggplant hydroxycinnamoyl CoA-quinate transferase (SmHQT), is a central enzyme that catalyzes the reaction to the chlorogenic acid production. Objective: The function of SmHQT is not well determined in the eggplant fruit, and the fruit agroinfiltration procedure is not standardized for eggplant. Materials and Methods: Here, the overexpression of SmHQT in the eggplant fruit´s flesh was studied using the agroinfiltration technique. In our gene construct, we also co-expressed the P19 protein for overexpression, and the results were validated with real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and high-performance liquid chromatography (HPLC). Results: Due to the overexpression of the SmHQT gene, higher chlorogenic content was exhibited by the eggplant fruits, which was further validated by HPLC. The chlorogenic acid content after following the agroinfiltration procedure was more two times in the agroinfiltrated fruit. To identify the optimal target for increasing chlorogenic pathway flux post-SmHQT activity, expression patterns were analyzed with qRT-PCR, and the results showed the changes in the expression level of the other chlorogenic acid pathway genes. Furthermore, the cis regulating elements and protein-protein interaction (PPI) analyses supported the HPLC results. Conclusion: Overall, here, insights into the eggplant chlorogenic content increment at the molecular level and the opportunities for the improvement of chlorogenic content as nutrition in crops are provided.