A double-layered conversion coating system, consisting of magnesium hydroxide–magnesium/manganese phosphate, was applied to magnesium alloy AZ91D using an acidic manganese nitrate and ammonium dihydrogen phosphate solution. The coating structure, composition and morphology were characterised by SEM, EDX, XRD and XPS. A coating formation mechanism is proposed, and the effect of operating parameters, i.e. pH and temperature, on coating formation was systematically investigated, with optimised conditions able to produce coatings of high corrosion resistance. Corrosion resistance of the coating was evaluated by electrochemical and salt spray testing. The double-layered coating system develops in three stages: initial substrate dissolution, formation of a dense magnesium hydroxide layer, and then co-deposition of magnesium and manganese phosphate film.