The synthesis and structural and magnetic characterization of the site-ordered double perovskites, Ba2Nd1-xMnxMoO6, 0 < x ≤ 1, are reported in order to show the effect of doping Jahn-Teller active, S = 1/2, Mo(5+) into the structure of Ba2MnMoO6, which exhibits anomalous long-range antiferromagnetic order. Rietveld refinements against room temperature neutron powder diffraction data indicate that the tetragonal distortion present in the Ba2NdMoO6 end member persists to x ≤ 0.3. This is predominantly manifested as a tilting of the MO6 octahedra, and there is no evidence of any structural phase transitions on cooling to 1.5 K. For x > 0.3, no deviation from the ideal cubic Fm3̅m symmetry is observed. Furthermore, dc-susceptibility measurements confirm that Mn(2+) is being doped onto the Nd(3+) site, and the associated oxidation of Mo(5+) to Mo(6+). For all compositions, the Curie-Weiss paramagnetic behavior above 150 K indicates negative Weiss constants that range from -24(2) and -85(2) K. This net antiferromagnetic interaction is weakest when x ≈ 0.5, where the disorder in cation site occupancy and competition with ferromagnetic interactions is the greatest. Despite these strong antiferromagnetic interactions, there is no evidence in the dc-susceptibility of a bulk cancellation of spins for x > 0.05. Low-temperature neutron diffraction measurements indicate that there is no long-range magnetic order for 0.1 ≤ x < 0.9. Ba2Nd0.10Mn0.90MoO6 exhibits additional Bragg scattering at 2 K, indicative of long-range antiferromagnetic ordering of the Mn(2+) cations, with a propagation vector k = (1/2, 1/2, 1/2). The scattering intensities can be modeled using a noncollinear magnetic structure with the Mn(2+) moments orientated antiferromagnetically along the four different ⟨111⟩ directions.