The area of the mosquito's microbiome has been attracting growing attention in the past decade. However, the direct relationship of collective microbiome-induced immune activation or inhibition on vector competence has not yet been explored in depth. The microbial diversity inside the mosquito host is determined by a variety of factors such as the blood meal, which also contributes to the anti-pathogen immune response inside the mosquito host. The interplay between host microbiota and the immune system actively influences the vector competence and consequently the transmission of pathogens by the arthropod vector. Symbiont bacteria and their key role in mosquito's biological processes are therefore promising candidates to be used in the control of vector-borne disease. Paratransgenesis describes the genetic modification of bacteria to produce effector molecules that can attenuate vector competence after being re-introduced inside the mosquito host.  In the current review, we provide an overview of the interaction between microbiota, the immune signalling, and implications of such interplay on the control of mosquito-borne diseases.