Acanthamoeba,a free-living amoeba (FLA) found in diverse ecosystems, poses significant health risks globally, particularly in Malaysia. It causes severe infectious diseases, e.g.,Acanthamoebakeratitis (AK), primarily affecting individuals who wear contact lenses, along with granulomatous amoebic encephalitis (GAE), a rare but often life-threatening condition among immunocompromised individuals. AK has become increasingly prevalent in Malaysia and is linked to widespread environmental contamination and improper contact lens hygiene. Recent studies highlightAcanthamoeba's capacity to serve as a "Trojan horse" for amoeba-resistant bacteria (ARBs), contributing to hospital-associated infections (HAIs). These symbiotic relationships and the resilience ofAcanthamoebacysts make treatment challenging. Current diagnostic methods in Malaysia rely on microscopy and culture, though molecular procedures like polymerase chain reaction (PCR) are employed for more precise detection. Treatment options remain limited due to the amoeba's cyst resistance to conventional therapies. However, recent advancements in natural therapeutics, including using plant extracts such as betulinic acid fromPericampylus glaucusand chlorogenic acid fromLonicera japonica, have shown promising in vitro results. Additionally, nanotechnology applications, mainly using gold and silver nanoparticles to enhance drug efficacy, are emerging as potential solutions. Further, in vivo studies and clinical trials must validate these findings. This review highlights the requirement for continuous research, public health strategies, and interdisciplinary collaboration to address the growing threat ofAcanthamoebainfections in Malaysia while exploring the country's rich biodiversity for innovative therapeutic solutions.