BackgroundMost studies in advanced care settings reported that the increasing workload increases the work-life imbalance and harms the mental health of health workers. The COVID-19 Pandemic's tracing, testing, treatment, and mass vaccination also have multiplied the primary healthcare workers' workload. Nevertheless, studies on primary care workers are scarce. This study aimed to investigate how the COVID-19-related work-life balance impact stress on primary healthcare workers in the third years of the pandemic.MethodsThe study was a cross-sectional, web-based survey conducted on primary healthcare workers in Kediri Regency, Indonesia, with the highest Omicron case surge worldwide. It was conducted right after the surge between July and August 2022, the third year of the COVID-19 pandemic hit Indonesia. Under coordination with the local government health officials, primary healthcare workers were invited to participate in an online survey. The respondents were asked to evaluate their sociodemography, work conditions, personal life, and perceived stress (using the Perceived Stress Scale) during the pandemic. Their work-life balance was evaluated using the Work/Non-work Interference and Enhancement Scale. We used several hierarchical linear regression models to determine which variables contribute to work stress among primary healthcare workers.ResultsSociodemographic characteristics, including gender, age, marital status, years of professional experience, and educational level, were not significantly associated with stress levels among our respondents. Separately, work conditions and personal life variables did not associate with stress levels. However, primary healthcare workers' work and personal lives interfere with each other during the pandemic and are associated with their higher stress.ConclusionDuring the pandemic, the work life of primary health workers interferes with their personal life more than the interference of personal life on their work life. At the same time, the work life's enhancement on the personal life and vice versa were lower than its interference. Those conditions are associated with higher perceived stress of primary health workers.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12913-023-09677-0.