We have fabricated two types of crosslinked chitosan-based nanoparticles (NPs), namely (1) ionically crosslinked with tripolyphosphate (TPP), designated as IC-NPs and (2) dually co-crosslinked (ionically and covalently with TPP and genipin, respectively) termed CC-NPs. The two types of NPs were physichochemically characterized by means of DLS-NIBS, synchrotron SAXS and M3-PALS (zeta potential). First, we found that covalent co-crosslinking of ionically pre-crosslinked nanoparticles yielded monodisperse CC-NPs in the size range of ∼200 nm, whereas the parental IC-NPs remained highly polydisperse. While both types of chitosan nanoparticles displayed a core-shell structure, as determined by synchrotron SAXS, only the structure of CC-NPs remained stable at long incubation times. This enhanced structural robustness of CC-NPs was likely responsible of their superior colloidal stability even in biological medium. Second, we explored the antimicrobial and quorum sensing inhibition activity of both types of nanoparticles. We found that CC-NPs had lower long-term toxicity than IC-NPs. In contrast, sub-lethal doses of IC-NPs consistently displayed higher levels of quorum quenching activity than CC-NPs. Thus, this work underscores the influence of the NP's ultrastructure on their colloidal and biological properties. While the cellular and molecular mechanisms at play are yet to be fully elucidated, our results broaden the spectrum of use of chitosan-based nanobiomaterialsin the development of antibiotic-free approaches against Gram-negative pathogenic bacteria.