The employ of nano-formulated biopesticides for mosquito control represents a promising strategy. Recently, it has been outlined that differences in the green reducing extracts used in nanosynthesis led to the production of nanoparticles with distinct bio-physical properities. In the present investigation, Hedychium coronarium-synthesized silver nanoparticles (AgNPs) were characterized by UV–vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), energy-dispersive X-ray diffraction (EDX), and transmission electron microscopy (TEM). The toxicity of H. coronarium rhizome extract and H. coronarium-synthesized AgNPs was assessed against larvae and pupae of the dengue vector Aedes aegypti, as well as against adults of the non-target copepod Mesocyclops formosanus. Then, the control of A. aegypti larval population was attempted using the predatory copepod M. formosanus in synergy with H. coronarium-synthesized silver nanoparticles, evaluating predation efficiency pre- and post-nanoparticle treatment. In presence of both predaceous copepods and nano-larvicides high control of the larval populations was obtained. Furthermore, histological changes in mosquitoes targeted with nanopesticides were studied by light microscopy, evaluating the impact on mid-gut epithelial cells following treatment with LC50 of AgNP. Overall, this study highlighted the concrete potential of synergizing copepod-based control programs with highly effective green nano-larvicides in the fight against dengue and Zika virus vectors.