We have demonstrated that three-dimensional (3D) surface engineering of silicon nanocrystals (SiNCs) by direct current microplasma processing in water with poly(3,4-ethylenedioxythiophene) doped by poly(styrenesulfonate) (PEDOT:PSS) can lead to nanocomposites with enhanced optoelectronic performance. Specifically, we have successfully shown improved photoluminescence properties of SiNCs inside water-based solution. The results also confirm that SiNCs become stable in water with potential application impact for biorelated applications. We have also shown that the microplasma processing in the presence of the polymer helps prevent the fast oxidation process over a longer period of time in comparison to the unprocessed sample. Furthermore, the assessment of transport properties confirmed the improvement of exciton dissociation after microplasma surface engineering; this can have direct implications for higher performance optoelectronic devices including solar cells.