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Background Several studies have shown that the impact of maternal mental health disorders on newborns’ well-being in low and middle-income countries (LMIC) are underreported, multi-dimensional and varies over time and differs from what is reported in high-income countries. We present the prevalence and risk factors associated with common mental disorders (CMDs) among breastfeeding mothers whose infants were admitted to Nigerian tertiary care facilities. Methods This was a national cross-sectional study involving mothers of hospitalised babies from eleven Nigerian tertiary hospitals. We used the WHO self-reporting Questionnaire 20 and an adapted WHO/UNICEF ten-step breastfeeding support package to assess mothers’ mental health and breastfeeding support. Results Only 895 of the 1,120 mothers recruited from eleven tertiary healthcare nurseries in six geopolitical zones of Nigeria had complete datasets for analysis. The participants’ mean age was 29.9 ± 6.2 years. One in four had CMDs; 24.0% (95% CI: 21.235, 26.937%). The ages of mothers, parity, gestational age at delivery, and length of hospital stay were comparable between mothers with and those without CMDs. Antenatal care at primary healthcare facilities (adjusted odds ratio [aOR:13], primary education [aOR:3.255] living in the south-southern region of the country [aOR 2.207], poor breastfeeding support [aOR:1.467], polygamous family settings [aOR:2.182], and a previous history of mental health disorders [aOR:4.684] were significantly associated with CMDs. In contrast, those from the middle and lower socioeconomic classes were less likely to develop CMDs, with [aOR:0.532] and [aOR:0.493], respectively. Conclusion In Nigeria, the prevalence of CMDs is relatively high among breastfeeding mothers with infants admitted to a tertiary care facility. Prior history of mental illness, polygamous households, mothers living in the southern region and low or no educational attainment have a greater risk of developing CMDs. This study provides evidence for assessing and tailoring interventions to CMDs among breastfeeding mothers in neonatal nurseries in LMIC.