HIV and AIDS represent a global public health issue with medical, social, and political implications. To meet the goal set by UNAIDS, it is necessary to gain a better understanding in France of the performance of our systems for monitoring and managing HIV infection. The objective of this study was to estimate the number of new HIV diagnoses in Nouvelle-Aquitaine during the 2015–2016 period and to document the differences observed between the two data sources: mandatory reporting (DO) and the Regional HIV Coordination Committees (CoreVIH) in this region. The number of new HIV diagnoses in Nouvelle-Aquitaine was estimated using a capture-recapture method with two data sources (mandatory reporting and CoreVIH). This study also included a qualitative component consisting of semi-structured individual interviews with healthcare professionals treating patients in the CoreVIH active patient registry, general practitioners, and volunteers from patient associations. This study estimated the completeness of the DO HIV registry in Nouvelle-Aquitaine at 65% (95% confidence interval [95% CI: 61.4–68.7]) and that of CoreVIH at 46% [43.6–48.8] in 2015–2016. Two main factors appear to affect the entry of new diagnoses into these databases: a decline in clinicians’ adherence to the DO since the rollout of mandatory electronic reporting (e-DO) and a delay in including patients in the CoreVIH database. Twenty-two interviews were conducted to explore the factors likely to cause delays in DO reporting or inclusion in the CoreVIH Aquitaine database. In conclusion, better dissemination of information and training efforts could improve the DO reporting and inclusion processes in the CoreVIH Nouvelle-Aquitaine database. The interviews identified areas for improvement in these domains that should be pursued. Finally, estimates of the number of new diagnoses must be updated regularly to meet public health needs.