Micro-injection moulding is one of the key manufacturing technologies for the batch production of miniaturized products made of thermoplastic polymers. However, the miniaturization is not simply based on the straightforward down scaling of the conventional injection moulding technique. Indeed, due to the reduction in sizes of the mould and the feed channels, very high shear rates stress the polymer melt in non-isothermal conditions, so that several issues can occur during the process and affect the final components. In this work, the relationships among the processing conditions, the mechanical properties and the microstructural characteristics of miniaturized specimens obtained by injection moulding were investigated. Two model systems were considered with the same filler content of 15% wt.: HDPE-talc and HDPE-glass beads, representative of two different filled micro-composites, namely lamellar and spherical. The attention was focused on the influence of the filler type and the process conditions on the mechanical behaviour, examined by uniaxial tensile tests, and on the microstructural characteristics of the specimens, examined by differential scanning calorimetry, polarized light microscopy and dynamic-mechanical thermal analysis. The results highlight that the mechanical response of the miniaturized specimens is significantly affected by both the filler and the mould temperature, due to the changing occurred in the sample microstructure. Lamellar composites showed the best performance due to the high orientation of the talc particles during the micro-injection process, while, different morphologies of the skin/core transition region based on the process temperatures were observable.