In this study, the morphological, thermal and electrical properties of microinjection-molded multi-walled carbon nanotubes (CNT)-filled poly(lactic acid) (PLA) and PLA/poly[(butylene succinate)-co-adipate] (PLA/PBSA) immiscible blends were studied systematically. The PLA/PBSA/CNT immiscible blends were prepared by melt blending of PLA, PBSA and CNT in a batch mixer. Four different types of compounding procedure were employed to investigate the influence of compounding sequence of various components on the electrical conductivity of subsequent micromoldings. Results revealed that despite the compounding sequence, the electrical conductivity of PLA/PBSA/CNT microparts is invariably higher than that of CNT-filled mono-PLA counterparts and the selective localization of CNT in PBSA is thought to be the contributing factor. Furthermore, the prevailing high shearing conditions in microinjection molding (A mu IM) could lead to the coalescence of CNT-enriched PBSA domains, favoring the formation of conductive pathways in the melt flow direction, as confirmed by morphology observations. The crystallinity of PLA/PBSA immiscible blends is higher than that of mono-PLA system and a further increase in crystallinity after A mu IM suggested flow-induced crystallization. Moreover, thermal stability analysis indicated that the prevailing high shear rates in A mu IM might have a chain scission effect on PLA and PBSA.