Combination of ink-jet printing (IJP) and micro-transfer moulding (µ-TM) micro-fabrication techniques is proposed and demonstrated in this work. First IJP is used to fill the micro-cavities in an elastomeric mould. Then a µ-TM process is done using this mould to transfer the pattern into a substrate. After optimization of the filling parameters, it has been possible to fabricate 60 µm-height test structures without any overflow or residual layer, with gaps of only 25 µm between them. Additionally, it is demonstrated that the proposed method can be used to manufacture heterogeneous structures in one single transfer step, after the deposition of more than one polymer into the mould. These results present the proposed IJP assisted µ-TM as an excellent candidate for the development of complex heterogeneous systems by means of a simple, robust and cost-efficient method.