One important aspect of the magneto-structural transition in MnCoGe-based materials is the reduction in saturation magnetization from the orthorhombic to the hexagonal phase. Here, by combining an element specific magnetization probe such as x-ray magnetic circular dichroism and band structure calculations, we show that the magnetic moment instability between orthorhombic and hexagonal structures originates from a reduction in the Mn sub-lattice magnetization.