Monitoring multiple cellular markers of immune cells may provide a more accurate evaluation of the immune status of people living with human immunodeficiency virus (PLHIV). This study assessed the value of CD16+CD56+ cells (NK cells) and CD19+ lymphocytes (B cells) phenotyping in indicating viral load, AIDS status, and treatment efficacy. A retrospective, laboratory-based study was conducted at the Diagnostic immunology division of a referral tertiary hospital. It involved 82 newly diagnosed HIV patients treated between 2009-2016. We explored three objectives: (1) the paired change in CD16+CD56+ and CD19+CD45+ cells counts and percentages from baseline to 2-to-6 months after treatment; (2) the association of these phenotypes with 5 gradual categories of viral load; and (3) the accuracy of CD16+CD56+ and CD19+CD45+ cells counts in indicating AIDS stage defined as CD4+ < 200 cells/mm3. The second and third objectives were tested using a pooled analysis (N = 300-373). The median CD19+CD45+ and CD16+CD56+ counts increased by 1.9-fold and 1.3-fold after treatment respectively (p < 0.001). A negative correlation of viral load with both CD16+CD56+ (ρ = -0.29, p < 0.001) and CD19+CD45+ (ρ = -0.34, p < 0.001) counts was observed. CD16+CD56+ count < 73 cells/mm3 and CD19+CD45+ count < 166.5 were indicative for AIDS with 95.5% and 63.6% sensitivity respectively. Findings advocate for the usefulness of CD16+CD56+ and CD19+CD45+ phenotyping in characterizing the severity of HIV infection and its impact on both the humoral and cellular immunity, as well as monitoring the effectiveness of treatment.