A systematic study of the magnetic and structural properties of manganese phthalocyanine thin films evaporated onto heated substrates in the temperature range from 260◦C to room temperature shows the disappearance of dynamic magnetic hysteresis loops below the measurement temperature of about 20 K. X-ray diffraction of manganese phthalocyanine thin films deposited onto electrically weakly interacting substrates shows a shift of the MnPc diffraction peak position from 7.1° to 6.8° as the deposition temperature is lowered. This crystalline peak shift is interpreted as a unit cell modification that is dependent on the substrate temperature during deposition. The dc susceptibility has a sharp increase below 18 K for the sample deposited at high temperature of 230◦C. Samples deposited at lower temperatures appear diamagnetic down to at least 5 K. The highest saturation magnetization of around 5μB per MnPc molecule is found for the sample deposited at 230◦C. The magnetic transition from the ferromagnetic ordering in manganese phthalocyanine thin films deposited at high-temperatures to possibly antiferromagnetic ordering for samples deposited at low temperatures correlates with structural changes. Additional manganese thin films co-deposited onto gold-coated substrates with a lying flat configuration do not show this transition at any deposition temperature. This corroborating evidence supports a structure-induced magnetic phase transition in differently prepared manganese phthalocyanine thin films.