Microinjection molding (µIM) is an emerging technology to fabricate microcomponents which could find ubiquitous applications in the areas of electronics, biomedical, automotive and microelectromechanical systems (MEMS). Compared with conventional molding technologies, µIM is characteristic of higher temperature gradients, higher shear rates and shorter cycle times. Recently, intensive research has been focused on investigating the properties of unfilled thermoplastics by µIM. However, there is increasing demand for multifunctional microparts which are always accommodated by using polymeric composites containing multifunctional fillers. The intrinsic properties of polymer matrices and added fillers as well as the interfacial interaction between fillers and the host matrix play a significant role in determining the dispersion of fillers within the host matrix. Thus, the effect of carbon fillers with different geometry (such as multi-walled carbon nanotubes, carbon black and graphite nanoplatelets) and the polymer matrices with different microstructure and polarity (i.e. polystyrene, polypropylene, polyamide 6 and polycarbonate) on the electrical and morphological properties of subsequent microparts was studied in detail. The distribution of carbon fillers within the microparts was evaluated by means of electrical conductivity measurements and morphology observations. Results indicated that the multi-walled carbon nanotubes and high structure carbon black are more effective than the graphite nanoplatelets in terms of enhancing the electrical conductivity of molded microparts. In addition, the electrical conductivity of microparts molded from carbon filler loaded polypropylene nanocomposites is always superior to that of other polymer/carbon counterparts, which was related to the morphology development in subsequent microparts. In summary, the development of microstructure was found to be strongly dependent on the types of carbon fillers used in µIM and their interfacial interaction with host polymers, which is essential to the enhancement of electrical conductivity for corresponding microparts.