Transition metal ion containing aluminophosphate molecular sieves with AlPO4-16 (AST) structure have been synthesized using the classic template, quinuclidine, and the corresponding salts of V4+, Co2+, Cr3+, and Mn2+. The cubic AST form was the main product. but in the presence of fluoride ions, the tetragonal AST form could also be obtained. The AST materials were characterized with X-ray diffraction, thermal analysis, scanning electron microscopy, electron spin resonance, infrared spectroscopy, and diffuse reflectance spectroscopy in the UV-vis-NIR region. Spectroscopic measurements showed that small amounts of Co2+ and Mn2+ can be incorporated in the framework. The diffuse reflectance spectra are indicative for the presence of two types of Co2+, most probably taking the two framework positions T-1 and T-2 with a T-1:T-2 occupation ratio of 3-8. In contrast, V4+ is present in defect sites by coordination to two (or three) framework oxygen atoms, The incorporation of Cr3+ in the AST framework is also uncertain and two surface Cr3+ species were observed: clusters similar to the bulk Cr2O3 oxide and isolated Cr3+ ions in strongly distorted octahedral coordination. These spectroscopic observations were confirmed by thermal analysis results, which showed that the degree of metal ion incorporation is inversely proportional with the phase transition temperature of AST to berlinite. Furthermore, Co2+ and V4+ are very stable in the AST structure and difficult to oxidize upon heating.