Neutron diffraction measurement on the spin glass double perovskite Sr2FeCoO6 reveals site disorder as well as Co3+ intermediate spin state. In addition, multiple valence states of Fe and Co are confirmed through M̈ossbauer and X-ray photoelectron spectroscopy. The structural disorder and multiple valence lead to competing ferromagnetic and antiferromagnetic interactions and subsequently to a spin glass state, which is reflected in the form of an additional T-linear contribution at low temperatures in specific heat. A clear evidence of Jahn-Teller distortion at the Co3+-O6 complex is observed and incorporating the physics of Jahn-Teller effect, the presence of localized magnetic moment is shown. A large, negative and anomalous magnetoresistance of ≈63% at 14 K in 12 T applied field is observed for Sr2FeCoO6. The observed magnetoresistance could be explained by applying a semi-empirical fit consisting of a negative and a positive contribution and show that the negative magnetoresistance is due to spin scattering of carriers by localized magnetic moments in the spin glass phase. © Springer-Verlag 2012.