The natural abundance, polymer stability, biodegradability, and natural antimicrobial properties of lignin open a wide range of potential applications aiming for sustainability. In this work, the effects of 1% (w/w) softwood kraft lignin nanoparticles (SLNPs) on the physicochemical properties of polybutylene succinate (PBS) composite films were investigated. Incorporation of SLNPs into neat PBS enhanced T_d from 354.1 °C to 364.7 °C, determined through TGA, whereas T_g increased from −39.1 °C to −35.7 °C while no significant change was observed in T_m and crystallinity, analyzed through DSC. The tensile strength of neat PBS increased, to 35.6 MPa, when SLNPs were added to it. Oxygen and water vapor permeabilities of PBS with SLNPs decreased equating to enhanced barrier properties. The good interactions among SLNPs, thymol, and PBS matrix, and the high homogeneity of the resultant PBS composite films, were determined through FTIR and FE-SEM analyses. This work revealed that, among the PBS composite films tested, PBS + 1% SLNPs + 10% thymol showed the strongest microbial growth inhibition against Colletotrichum gloeosporioides and Lasiodiplodia theobromae, both in vitro, through a diffusion method assay, and in actual testing on active packaging of mango fruit (cultivar “Nam Dok Mai Si Thong”). SLNPs could be an attractive replacement for synthetic substances for enhancing polymer properties without compromising the biodegradability of the resultant material, and for providing antimicrobial functions for active packaging applications.