Antiretroviral therapy (ART) has significantly improved the life expectancy of people living with HIV-1 (PLWH). However, prolonged ART use is linked to metabolic alterations and oxidative stress. The paraoxonase (PON) enzymes, especially PON-1 and PON-2, are critical in maintaining antioxidant balance. Their activity can be influenced by polymorphisms such as Q192R and L55M in PON-1 and A148G and S311C in PON-2. This study examines the impact of these polymorphisms on paraoxonase activity, lipid metabolism, and infection markers in PLWH under various ART regimens. This is a case-control study with 525 participants, 175 healthy controls (HC) and 350 PLWH divided into subgroups: T0 (ART-naïve, = 48), T1 (ART with reverse transcriptase inhibitors, = 159), and T2 (ART with protease inhibitors, = 143). Paraoxonase activity was higher in PLWH (123.0; IQR: 62.0-168.0) compared to HC (91.0; IQR: 48.0-136.0, < 0.001) but similar between HC and T0 ( = 0.594). T1 (125.0; IQR: 65.5-166.0) and T2 (123.0; IQR: 61.0-182.0) showed higher activity than HC ( = 0.002 and 0.003). Among 61 complete genotypes, 13 were unique to PLWH and 6 to HC ( < 0.001). L55L was more frequent in HC (49.7% vs. 36.9% in PLWH), while M55M was higher in PLWH ( = 0.004). The S311C genotype was more frequent in HC (39.2%) than PLWH (24.9%) ( = 0.003). The L55L genotype conferred 59.9% protection against HIV-1 (OR: 0.401; 95% CI: 0.228-0.704), while the M allele increased susceptibility by ~69% (OR: 1.694; 95% CI: 1.173-2.446). The M55M genotype and/or M allele may be linked to HIV-1 susceptibility. Prolonged ART use elevates PON-1 activity in PLWH.