Despite the reduced human immunodeficiency virus (HIV) disease burden in Nigeria and globally, the key populations (KPs) can be disproportionately burdened with HIV infection and lower treatment coverage and outcome. A viral load (VL) test is needed to monitor the treatment outcome of KP with VL suppression of < 1000 copies/mL, demonstrating a positive treatment outcome. For unsuppressed VL, enhanced adherence counseling (EAC) may improve viral suppression in people living with HIV/KPs living with HIV (PLHIV/KPLHIV). Conventionally, EAC sessions are done for 3 months through physical visits. Due to the challenges of monthly visits (including transportation, socioeconomic status, and high mobility among KPs), other EAC delivery models need to be explored. We aimed to assess the effect of phone EAC sessions among virally unsuppressed KPs compared to physical EAC. Using a prospective intervention study design with a sample size of 484, unsuppressed KPLHIV in Delta State Nigeria were selectively stratified (non-randomized) using a simple stratification (ability vs. inability to physically attend EAC sessions in-person) into an intervention group and a control group, receiving phone-based EAC sessions and physical EAC sessions respectively. Repeated VL tests were done 3 months after the intervention, and viral suppression was pegged at the WHO recommendation of <1000 copies/mL. The SPSS version 24.0 (SPSS Inc., Chicago, USA) was used for data analysis of variables within and between study groups. Significance was interpreted at p < 0.05. Participants were 87.4% males {out of which 75.0% (363/484) identified as men who have sex with men (MSM)} with a mean age of 26 ± 2 years. The intervention group had a slightly higher EAC completion rate at 99.6% than the control group (97.9%). Both groups showed significant differences in viral suppression from 0% to a mean suppression of 88.7% with p < 0.01. The intervention group achieved better suppression (90.5%) than the control group (86.7%). EAC effectively achieves viral suppression by up to 90% among KPLHIV. Phone-based EAC has also proven effective and, in our findings, slightly more effective than the conventional physical EAC and is recommended among KPLHIV with the known challenge of transportation or poor mobility.