A novel combination of ink-jet printing (IJP) and micro-transfer moulding (μ-TM) for high-resolution, heterogeneous material microstructuring is demonstrated. First, IJP is used to accurately fill the micro-cavities in an elastomeric mould, thus avoiding the use of spin coating or direct casting with a noticeable reduced material waste. Second, a μ-TM process is performed using the as-filled mould to transfer the patterns onto another substrate. After optimizating the filling parameters, it was possible to fabricate 60 μm-high test structures with gaps down to 25 μm between them. Additionally we also used the IJP to deposit different polymers in the same mould in order to create heterogeneous structures in one single transfer step. We present details on the mould filling characteristics by IJP and capillary forces, and show a potential application example by using Lilac and Yellow doped epoxy polymers as possible optical waveguide filtering structures. These results show that the IJP assisted μ-TM is an excellent candidate for the low-waste and cost-effective manufacturing of complex heterogeneous polymer microsystems.