The Epstein-Barr Virus (EBV) encodes viral microRNAs (miRs) that contribute to the pathogenesis of nasopharyngeal and gastric carcinomas, but their potential roles in lymphomas are still to be elucidated. This study sought to assess the impact of knocking down EBV miRs BART 7 and BART9 in EBV-positive Akata cell lines using CRISPR/Cas9 technology. Compared to cells harboring the wild-type (WT) EBV genomes, Akata cells subjected to CRISPR/Cas9-mediated knockdown of EBV BART 7 and BART9 showed a significant reduction in the expression of viral miRs, confirming the validity of the experimental model. Knocking down both BART7 and BART9 caused a significant reduction in cell viability and proliferation rates while increasing the expression of EBV lytic genes. Global proteomic analysis shows that knocking down EBV BART7 significantly decreased the expression of ubiquitin/proteasome proteins while increasing RNA binding proteins (RBPs). On the other hand, BART9 knockdown caused a decrease in proteins associated with oxidoreductase activity, including the metabolism of fatty acids. Our results unravel previously unknown roles for EBV miRs BART7 and BART9 on cellular pathways relevant to both viral biology and lymphomagenesis.