We report on systematic ab initio investigations of Co and Cr interlayers embedded in Fe(001)/MgO/Fe(001) magnetic tunnel junctions, focusing on the changes in the elctronic structure and the transport properties with interlayer thickness. The results of spin-dependent ballistic transport calculations reveal options to specifically manipulate the tunnel magnetoresistance ratio. The resistance-area products and the tunnel magnetoresistance ratios show a monotonous trend with distinct oscillations as a function of Cr thickness. These modulations are directly addressed and interpreted by means of magnetic structures in the Cr films and by complex band-structure effects. The characteristics for embedded Co interlayers are considerably influenced by interface resonances which are analyzed by the local electronic structure.