In 2011, Chile added 12 mandatory extra weeks of maternity leave (ML). In January 2015, a pay-for-performance (P4P) strategy was included in the primary healthcare system, incorporating exclusive breastfeeding (EBF) promotion actions. The COVID-19 pandemic led to healthcare access difficulties and augmented household workloads. Our aim was to evaluate the effect of a 24-week ML, the P4P strategy, and COVID-19 on EBF prevalence, at 3 and 6 months in Chile. Aggregated EBF prevalence data from public healthcare users nationwide (80% of the Chilean population) was collected by month. Interrupted time series analyses were used to quantify changes in EBF trends from 2009 to 2020. The heterogeneity of EBF changes was assessed by urban/setting and across geographic settings. We found no effect of ML on EBF; the P4P strategy increased EBF at 3 months by 3.1% and 5.7% at 6 months. COVID-19 reduced EBF at 3 months by  − 4.5%. Geographical heterogeneity in the impact of the two policies and COVID-19 on EBF was identified. The null effect of ML on EBF in the public healthcare system could be explained by low access from public healthcare users to ML (20% had access to ML) and by an insufficient ML duration (five and a half months). The negative impact of COVID-19 on EBF should alert policy makers about the crisis's effect on health promotion activities.