A hydrotropic solution of maleic acid (MA) was exploited to fractionate giant reed (AD) and eucalypt (EUC). The pre-treatment was successful for AD, while it was unsatisfactory for EUC, likely due to unoptimized reaction conditions. Interestingly, lignin nanoparticles (LNP) were produced via spontaneous aggregation following spent liquor dilution. LNP were studied by a plethora of analytical techniques, such as thermogravimetry, electron microscopy, and Nuclear Magnetic Resonance spectroscopy (NMR). Notwithstanding LNP from both AD and EUC showed similar thermal behaviour and morphology, a greater content of aliphatic hydroxyl, carboxyl, guaiacyl and p-hydroxyphenyl moieties was reported for AD-LNP, whereas EUC-LNP had a larger amount of syringyl groups and a higher S/G ratio. Also, the 1H-DOSY NMR indicated the lower size of AD-LNP. Moreover, the LNP were found to negatively impact on the development of several human or plant pathogens, and their bioactivity was related to the occurrence of guaiacyl and p-hydroxyphenyl moieties and a lower the LNP size. We therefore found that MA delignification allows both to achieve high delignification efficiency and to obtain LNP with promising antibacterial effect. Such LNP may help counteracting the antibiotics resistance and sustain the quest for finding sustainable agrochemicals.