Green compost represents a sustainable source of humic substances (HS), which are supramolecular associations of heterogeneous natural compounds bearing a variety of functional groups. Novel humic-chitosan nanoconjugates (NC) were synthesized by using HS from three green composts [coffee husks (HS-COF), artichoke residues (HS-CYN), and fennel residues (HS-FEN)]. Solid-state NMR spectra showed that HS-CYN and HS-FEN contained the largest relative amount of polysaccharidic and phenolic carbons, whereas HS-COF had the greatest relative content of alkyl and carboxyl groups. While size and z-potential of NC depended upon the HS origin, NC-HS-FEN revealed the greatest thermal stability, followed by NC-HS-CYN and NC-HS-COF. Scanning electron microscopy and transmission electron microscopy analyses suggested the formation of spherical nanoparticles only for NC-HS-FEN and NC-HS-CYN. This was explained by more stable conformations of HS-FEN and HS-CYN that enabled regular spherical nanoparticles, as assessed by high-pressure size-exclusion chromatography measurements. NC bioactivity against bacterial human pathogens was strain-specific, and the inhibition of bacterial development was attributed to the positive z-potentials that facilitated NC adhesion on bacterial cell walls, smaller nanosizes favoring cell penetration, and subsequent release in the cell of NC toxic components that altered microbial biochemical functions. This study indicates that not only novel NCs can be obtained by humic matter derived from recycled biomass, such as green compost, but they can also be employed as effective and sustainable antimicrobial agents.