Background Essential newborn care (ENC) covers optimal breastfeeding, thermal care, and hygienic cord care. These practices are fundamental to save newborn lives. Despite neonatal mortality remaining high in some parts of Peru, no comprehensive data on ENC is available. We sought to estimate the prevalence of ENC and assess differences between facility and home births in the remote Peruvian Amazon. Methods We used baseline data from a household census of rural communities of three districts in Loreto region, collected as part of the evaluation of a maternal-neonatal health (MNH) programme. Women between 15 and 49 years with a live birth in the last 12 months were invited to complete a questionnaire about MNH-related care and ENC. Prevalence of ENC was calculated for all births and disaggregated by place of birth. Adjusted prevalence differences (PD) were post-estimated from logistic regression models on the effect of place of birth on ENC. Findings All 79 rural communities with a population of 14,474 were censused. Among 324 (>99%) women inter-viewed, 70% gave birth at home, most (93%) without skilled birth assistance. Among all births, prevalence was lowest for immediate skin-to-skin contact (24%), colostrum feeding (47%), and early breastfeeding (64%). ENC was consistently lower in home compared to facility births. After adjusting for confounders, largest PD were found for immediate skin-to-skin contact (50% [95% CI: 38-62]), colostrum feeding (26% [16-36]), and clean cord care (23% [14-32]). ENC prevalence in facilities ranged between 58 and 93%; delayed bathing was lower compared to home births (-19% [-31 to -7]). Interpretation Low prevalence of ENC practices among home births in a setting with high neonatal mortality and difficult access to quality care in facilities suggests potential for a community-based intervention to promote ENC practices at home, along with promotion of healthcare seeking and simultaneous strengthening of routine facility care.