This study explores the control of Al location in zeolites by organic structure-directing agents (OSDAs) using atomistic simulations. We examine several zeolite–OSDA complexes to quantify the Al site-directing ability. The results show that OSDAs induce different energetic preferences to direct Al at certain locations. In particular, these effects can be enhanced by OSDAs with N–H moieties. Our findings will be useful for the development of novel OSDAs that can modulate Al site-directing properties.