We present extensive temperature dependent (16–70 K) magnetic and electric molecular beam deflection measurements on neutral manganese doped tin clusters Mn/Sn_N (N = 9–18). Cluster geometries are identified by comparison of electric deflection profiles and quantum chemical data obtained from DFT calculations. Most clusters adopt endohedral cage structures and all clusters exhibit non-vanishing magnetic dipole moments. In the high temperature regime all species show exclusively high field seeking magnetic response and the magnetic dipole moments are extracted from the shift of the molecular beam. At low nozzle temperatures, some of the clusters show considerably broadened beam profiles due to non-uniform deflection in the magnetic field. The results reflect the influence of the chemical environment on the magnetic properties of the transition metal in atomic domain magnetic nanoalloys. Different ground state spin multiplicities and coupling of rotational and vibrational degrees of freedom with the spin angular momentum of isolated clusters of different size apparently cause these variations of spin orientation. This is discussed by taking electronic and molecular structure data into account.