Background Although treatment adherence is a major challenge in sub-Saharan Africa, it is still unknown which longitudinal patterns of adherence are the most detrimental to long-term virological response to non-nucleoside reverse transcriptase inhibitor (NNRTI) regimens. This analysis aimed to study the influence of different time patterns of adherence on virological failure after 24 months of treatment in Cameroon. Methods Antiretroviral therapy (ART) adherence data were collected using face-to-face questionnaires administered at months 1, 3, 6, 12, 18 and 24. Virological failure was defined as viral load >40 copies/ml at month 18 and/or 24. Two combined indicators of early adherence (months 1, 3 and 6) and adherence during the maintenance phase (months 12, 18 and 24) were designed to classify patients as always adherent during the early or maintenance phase, non-adherent at least once and having interrupted ART for >2 days at least once at any visit during either of these two phases. Results Virological failure occurred in 107 (42%) of the 254 patients included in the analysis. In the early and maintenance phases, 84% and 76%, respectively, were always adherent, 5% and 5% were non-adherent and 11% and 20% experienced ≥1 treatment interruption. Early non-adherence was independently associated with virological failure (adjusted OR 7.2 [95% CI 1.5, 34.6]), while only treatment interruptions had a significant impact on virological failure during the maintenance phase (adjusted OR 2.1 [95% CI 1.1, 4.4]). Conclusions ART NNRTI-regimens used in sub-Saharan Africa seem to ‘forgive’ deviations from good adherence during the maintenance phase. Optimizing adherence in the early months of treatment remains crucial, especially in a setting of poor health care infrastructure and resources.