The structure and superconducting properties of ammoniated calcium-graphite intercalation compound (Ca-GIC) have been investigated using in situ time-of-flight neutron diffraction, Raman spectroscopy and magnetization studies. Ammonia absorption has been carried out by exposing preformed Ca-GIC to ammonia vapour at various pressures. Our in situ neutron diffraction data reveal a complex ammonia pressure dependent structural transformation, in which the growth of secondary ammoniated Ca-GIC phases are observed at the expense of the pristine CaC(6) and graphite. The ammonia absorption is irreversible in nature, and degassing the sample at elevated temperature leads to the formation of calcium amide and hydrogen. The Raman spectroscopy and magnetization studies show that the ammonia absorption not only leads to a large stacking disorder, but it also reduces the superconducting CaC(6) phase fraction. Finally, we propose a molecular stacking model which accounts for the observed ammonia absorption and concomitant structural phase transitions.