We investigate, using periodic quantum mechanical calculations, how different counterions affect the geometrical and electronic structure of Al3+ and Fe3+ active sites in zeolites and AIPOs. Association of the counterion with one or more framework oxygens modifies their bond lengths within the framework, including the distance from the dopant ion, and hence the symmetry of the active sites. The average bond length of the dopant with its four oxygen neighbors is, however, only marginally affected by the type of counterion. We further find that the presence of framework dopants influences the electronic structure, and in particular that low-valent dopant ions are ionic, while causing an increase of covalence in the surrounding region of the framework.