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 Tg and Td from −39.1 °C to −35.7 °C and 354.1 °C to 364.7 °C, respectively, determined through TGA, whereas no significant change was observed in Tm and crystallinity, analyzed through DSC. The tensile strength of neat PBS significantly increased, to 35.6 MPa, when SLNPs were added to it. Oxygen and water vapor permeabilities of PBS with SLNPs decreased to 1.59 × 10−3 cm3 m h−1 m−2 atm−1 and 1.41 × 10−3 g m h−1 m−2 atm−1 compared with neat PBS with 2.28 × 10−3 cm3 m h−1 m−2 atm−1 and 1.54 × 10−3 g m h−1 m−2 atm−1, respectively, 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.