The high burden of anaemia during pregnancy underscores the urgent need to gain a comprehensive understanding of the factors contributing to its widespread occurrence. Our study assessed the prevalence and the trends of moderate-to-severe anaemia (MSA) in late pregnancy (28 to 36 weeks) and then investigated the key determinants driving this prevalence among women in Lagos, Nigeria. We conducted a secondary data analysis involving 1216 women enrolled in the Predict-PPH study between January and March 2023. We employed a multivariate binary logistic regression model with a backward stepwise selection approach to identify significant predictors of MSA. The study revealed a 14.5% prevalence of MSA during pregnancy. Independent predictors of MSA included having given birth to two or more children (adjusted odds ratio = 1.46, 95% confidence interval: 1.03–2.07), having a maternal body mass index (BMI) of 28 kg/m2 or higher (adjusted odds ratio = 1.84, 95% confidence interval: 1.29–2.61), having less than tertiary education (adjusted odds ratio = 1.51, 95% confidence interval: 1.08–2.11), and being unemployed (adjusted odds ratio = 1.97, 95% confidence interval: 1.19–3.26). It is crucial for pregnant women, particularly those with higher parities and elevated BMI, to be monitored regularly for anaemia and its consequences during their antenatal care. Additionally, addressing the link between low education, unemployment, and anaemia necessitates comprehensive strategies that empower women in terms of education and economic status to enhance the overall well-being of individuals and communities, ultimately reducing the prevalence of anaemia and associated health issues in pregnancy.