Intracellular symbiosis impacts many aspects of insect biology, and disruption of these symbioses is a novel insect-pest-control strategy. Horizontally transferred genes (HTGs) are critical for insect-intracellular symbiont association, representing candidate molecular targets for symbiosis disruption. However, few studies have tested this in the laboratory and under field conditions. Biotin and lysine HTGs are involved in Bemisia tabaci MEAM1 symbiosis persistence. In this study, we showed that whitefly biotin and lysine genes can be silenced by the tobacco rattle virus (TRV), a tobravirus. Then, we demonstrated that the vector 2mDNA1, an engineered begomovirus transmitted by B. tabaci, was effective for silencing B. tabaci MED HTGs in the laboratory. The 2mDNA1-silencing biotin HTGs reduced levels of biotin, as well as survival, fecundity, and population increases of whiteflies. The 2mDNA1-silencing biotin HTGs did not impact the titers of symbionts in F0 whiteflies but decreased the titers of symbiont Portiera in F2 whiteflies. The 2mDNA1-silencing lysine HTG reduced levels of lysine, titers of Portiera in both F0 and F2 whiteflies as well as the survival, fecundity, and population increases of whiteflies. The 2mDNA1-mediated silencing of whitefly genes is horizontally transmitted among whiteflies, enhancing the effectiveness of gene silencing. We further revealed that the vector 2mDNA1 can be used to silence whitefly HTGs and inhibit whitefly performance in the greenhouse. This study demonstrates that repressing the expression of insect HTGs though a modified virus is feasible for the control of phloem-feeding insect pests.