BackgroundAnaemia in pregnancy (AIP) remains a severe public health problem associated with adverse outcomes. This study assessed haemoglobin levels and the prevalence of anaemia during antenatal care (ANC) registration, at 28 weeks and 36 weeks of gestation as well as the factors associated with AIP at the different stages of pregnancy.MethodsA retrospective cross-sectional design was implemented. Using ANC registers as the sampling frame, 372 pregnant women, within 36 and 40 weeks of gestation were randomly sampled from 28 health facilities for the study. The participants were all receiving ANC in the Bolgatanga Municipality. Data were collected via clinical records review and a questionnaire-based survey between October and November, 2020. Using the Statistical Package for the Social Sciences (SPSS), descriptive analysis of haemoglobin levels and the prevalence of anaemia were performed. In addition, binary logistic regression was used to identify the factors associated with anaemia in pregnancy. AIP was determined using the national practice of 11.0g/dl haemoglobin cut-off point and the World Health Organisation’s recommended adjustment for the 2ndtrimester of pregnancy was made using the cut-off of 10.5g/dl to account for the effect of haemodilution.ResultsAt booking, AIP prevalence was 35.8% (95%CI:30.9, 40.9) using a cut-off of 11.0g/dl and 25.3% (95%CI:20.9, 30.0) using a cut-off of 10.5g/dl for those in the 2ndtrimester. At 28 weeks, AIP prevalence was 53.1% (95%CI:45.8, 60.3) and 37.5 (95%CI:30.6, 44.8) using a cut-off of 11.0g/dl and 10.5g/dl for those in the 2ndtrimester, respectively. At 36 weeks, AIP prevalence was 44.8% (95%CI:39.2, 50.4) using a cut-off of 11.0g/dl. At p<0.05, registering after the first trimester (AOR = 1.87, 95%CI: 1.17, 2.98, P = 0.009) and at a regional hospital (AOR = 2.25, 95%CI: 1.02, 4.98, P = 0.044) were associated with increased odds of AIP but registering at a private hospital (AOR = 0.32, 95%CI: 0.11, 0.92, P = 0.035) was associated with decreased odds of AIP at booking. At 28 weeks, age group 26–35 years (AOR = 0.46, 95%CI: 0.21, 0.98, P = 0.044), Christianity (AOR = 0.32, 95%CI: 0.31, 0.89, P = 0.028.), high wealth (AOR = 0.27, 95%CI: 0.09, 0.83, P = 0.022) and tertiary education (AOR = 0.09, 95%CI:0.02, 0.54, P = 0.009) were associated with decreased odds of AIP. At 36 weeks, booking after first trimester of pregnancy was associated with increased odds (AOR = 1.72, 95%CI: 1.05, 2.84, P = 0.033) whilst high wealth (AOR = 0.44, 95%CI: 0.20, 0.99, P = 0.049), higher age groups—26–35 (AOR = 0.38, 95%CI: 0.21, 0.68, P = 0.001) and 36–49 years (AOR = 0.35, 95%CI: 0.13, 0.90, P = 0.024) and secondary education of spouse were associated with reduced odds (AOR = 0.35, 95%CI: 0.14, 0.88, P = 0.026) of AIP.ConclusionAIP consistently increased from registration to 36 weeks of gestation. Given the observed correlates of AIP, we recommend that interventions geared towards early ANC registration, improved household wealth, and improved maternal education are required to reduce AIP.