Objectives Accurate civil registration and vital statistics (CRVS) systems are the primary data source to measure the impact of the COVID-19 pandemic on mortality. This study assesses how the pandemic impacted CRVS system processes in Loreto region of Peru, one of the worst affected countries globally. Design Qualitative study. Setting Loreto, a remote region, which had the highest reported mortality rate in Peru during the pandemic. Participants Semistructured individual interviews and documentary analysis were conducted between September 2020 and May 2021 with 28 key informants from eight institutions involved in death certification. Key informants were identified using a purposive sampling strategy commencing at the Health Directorate of Loreto, and the snowball method was used where a participant suggested another organisation or person. Information from key informants was used to compare business process maps of the CRVS system before and during the pandemic. Results During early May 2020, there were seven times more registered deaths than in earlier years, but key informants believed this underestimated mortality by 20%-30%. During the pandemic, families had to interact with more institutions during the death certification process. Several issues disrupted death certification processes, including the burden of increased deaths, the Environmental Health Directorate often removing a body without the family's express agreement, the creation of COVID-19 cemeteries where no death certificate was needed for burial, greater participation of funeral homes that often used outdated paper forms, and closure of civil registry offices. There was increased use of the online National Death System (SINADEF) but many users had problems with access. Conclusions The pandemic substantially disrupted CRVS processes in Loreto, making death certification more difficult, placing greater burden on the family and leading to more participation from unregulated organisations such as funeral homes or cemeteries. These disruptions were impacted by limitations of the CRVS system's processes before the pandemic.