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Comparative studies of structure, magnetism, and magnetoresistance (MR) have been carried out in A-site ordered NdBaMn2O6 (O-NB), A-site disordered NdBaMn2O6 (D-NB) and A-site disordered NdCaMn2O6 (D-NC). O-NB, where A-site cations, Nd3+ and Ba2+ (of different ionic sizes) are arranged periodically, undergoes structural transition with temperature, while no structural change is present in D-NB where A-site cations are arranged randomly. However, structural transitions are observed in D-NC where Nd3+ and Ca2+ have similar ionic sizes. Magnetization (M) data shows O-NB has AFM ground state associated with a lower structurally symmetric phase and an FM ground state is observed for D-NB with higher structural symmetry. However, AFM ground state is observed in D-NC similar to that of O-NB. Both the disorder systems exhibit semiconductive transport characteristics over the entire temperature range. The resistivity data of disorder compounds have been fitted with different theoretical models to elucidate the conduction process in these systems. Further, MR studies depict a three times higher value of MR in both disorder compounds compared to that of order one. However, the behavior of MR with H is different for D-NB and D-NC, implying a different origin of this large MR in these compounds. We believe that the different magnetic ground state of D-NB and D-NC is the possible origin of their distinct MR behavior to the magnetic field.