We investigate the effects of polymer chains and nanoparticles on the deformation of a droplet in shear and extensional flow using computational modeling that accounts for both the solid and fluid phases explicitly. We show that under shear flow, both the nanoparticles and the encapsulated polymers reduce the shear-induced deformation of the droplet at intermediate capillary numbers. At high capillary numbers, however, long polymer chains can induce the breakup of the droplet. We find that the latter behavior is dependent on the nature of the imposed flow. Specifically, under extensional flow, long polymers inhibit the droplet breakup and reduce deformation. Overall, the findings provide guidelines for tailoring the stability of filled droplets under an imposed flow, and thus, the results can provide useful design rules in a range of technological applications.