We report on molecular simulations of zinc oxide nanostructures obtained within silica nanopores of diameter D = 1.6 nm and D = 3.2 nm. Both the effects of confinement (by varying the pore size) and degree of pore filling on the structure of the nanomaterial are addressed. Two complementary approaches are adopted: 1) the stability of the three crystalline phases of ZnO (wurtzite, rocksalt, and blende) in the silica nanopores is studied, and 2) ZnO nanostructures are obtained by slowly cooling down a homogeneous liquid phase confined in the silica pores. None of the ideal nanostructures (wurtzite, rocksalt, blende) retains the ideal structure of the initial crystal when confined within the silica pores. Only the structure starting from the ideal wurtzite nanocrystal remains significantly crystalline after relaxation, as revealed by the marked peaks in the pair correlation functions for this system. The morphology and degree of cristallinity of the structures are found to depend on the parameters involved in the synthesis (pore size, filling density). Nanograin boundaries are observed between domains of different crystal structures. Reminiscent features of the bulk behavior, such as faceting of the nanostructures, are also observed when the system size becomes large. We show that the use of nanopores as a template imposes that the confined particles exhibit neutral (basal) surfaces. These predictions provide a guide to experiments on semiconductor nanoparticles.