Transition metal diboride-based thin films are currently receiving strong interest in fundamental and applied research. Multilayer thin films based on transition metal diborides are, however, not yet explored in detail. This study presents results on the constitution and microstructure of multilayer thin films composed of TiBx and the intermetallic compound NiAl. Single layer NiAl and TiBx and NiAl/TiBx multilayer thin films with a variation of the individual layer thickness and bilayer period were deposited by D.C. and R.F. magnetron sputtering on silicon substrates. The impact of the operation mode of the sputtering targets on the microstructure of the thin films was investigated by detailed compositional and structural characterization. The NiAl single layer thin films showed an operation mode-dependent growth in a polycrystalline B2 CsCl structure with a cubic lattice with and without preferred orientation. The TiBx single layer thin films exhibited an operation mode independent crystalline structure with a hexagonal lattice and a pronounced (001) texture. These TiBx layers were significantly Ti-deficient and showed B-excess, resulting in stoichiometry in the range TiB2.64–TiB2.72. Both thin film materials were deposited in a regime corresponding with zone 1 or zone T in the structure zone model of Thornton. Transmission electron microscopy studies revealed, however, very homogeneous, dense thin-film microstructures, as well as the existence of dislocation lines in both materials. In the multilayer stacks with various microscale and nanoscale designs, the TiBx layers grew in a similar microstructure with (001) texture, while the NiAl layers were polycrystalline without preferred orientation in microscale design and tended to grow polycrystalline with (211) preferred orientation in nanoscale designs. The dislocation densities at the NiAl/TiBx phase boundaries changed with the multilayer design, suggesting more smooth interfaces for multilayers with microscale design and more disturbed, strained interfaces in multilayers with nanoscale design. In conclusion, the volume fraction of the two-layer materials, their grain size and crystalline structure, and the nature of the interfaces have an impact on the dislocation density and ability to form dislocations in these NiAl/TiBx-based multilayer structures.