This article examines the effect of biometric attendance management on human resource governance (HRG) in selected private universities in Uganda. The study addresses a governance paradox: biometric clocking can strengthen attendance traceability and reduce manipulation, yet university work includes research, supervision, preparation, online engagement, assessment and community service that may occur outside fixed clocking points. A cross-sectional mixed-methods design was used, with a dominant quantitative component analysed using partial least squares structural equation modelling (PLS-SEM) and an explanatory qualitative component analysed thematically. From a target population of 1,218 employees and institutional actors, the intended sample was 301 respondents; the final SmartPLS analysis used 289 complete observations. Attendance Management had a statistically significant negative association with HRG (β = −0.505, t = 3.845, p < .001, 95% CI [−0.816, −0.308]), with a medium effect size (f² = 0.329). The qualitative evidence explained this counterintuitive result through five interconnected themes: attendance accountability, academic work invisibility, system reliability, policy clarity and procedural fairness, and fair performance evaluation. The findings indicate that biometric attendance can support HR governance when it is reliable, transparent and context-sensitive, but may weaken perceived governance when it operates as rigid time-control or when technical errors and narrow attendance records are used punitively. The article recommends hybrid attendance governance that combines biometric records with workload evidence, correction and appeal procedures, staff communication and broader indicators of academic performance.