At interfaces between complex oxides, electronic, orbital and magnetic reconstructions may produce states of matter absent from the materials involved, offering novel possibilities for electronic and spintronic devices. Here we show that magnetic reconstruction has a strong influence on the interfacial spin selectivity, a key parameter controlling spin transport in magnetic tunnel junctions. In epitaxial heterostructures combining layers of antiferromagnetic LaFeO(3) (LFO) and ferromagnetic La(0.7)Sr(0.3)MnO(3) (LSMO), we find that a net magnetic moment is induced in the first few unit planes of LFO near the interface with LSMO. Using X-ray photoemission electron microscopy, we show that the ferromagnetic domain structure of the manganite electrodes is imprinted into the antiferromagnetic tunnel barrier, endowing it with spin selectivity. Finally, we find that the spin arrangement resulting from coexisting ferromagnetic and antiferromagnetic interactions strongly influences the tunnel magnetoresistance of LSMO/LFO/LSMO junctions through competing spin-polarization and spin-filtering effects.