The investigation of therapeutic agents for Acanthamoeba keratitis (AK) is necessary as nonspecific, toxic, and long-lasting treatments are currently found. In this study, ß-caryophyllene was selected as an anti-Acanthamoeba candidate due to its known antiinflammatory and analgesic activities, which are pharmacological actions desirable for this application. On the other hand, this sesquiterpene presents a low aqueous solubility, high volatility, and susceptibility to oxidation, which motivated its incorporation into polymeric nanoparticles (NPs). Chitosan (CS) was selected as the biopolymer due to its bioadhesive properties and wide use in ophthalmic preparations, which was cross-linked with tripolyphosphate (TPP) to obtain stable particles. Monodisperse NPs with reduced size (<245 nm) and presenting a positive surface charge (ζpotential between +15.23 and +18.15 mV) were obtained regardless of the type of chitosan selected. The colloidal suspensions were stable for up to 60 and 90 days after storage at 25 and 4 °C, respectively. The nanoencapsulation of ß-caryophyllene led to a series of benefits: (a) increased its activity against Acanthamoeba castellanii trophozoites; (b) reduced corneal toxicity as no more collagen disruption was found in the stroma; and (c) increased retention and mucoadhesion in corneal tissue. In view of these positive results, in vivo studies are encouraged, as well as formulation studies including potential therapeutic agents in this same nanocarrier.