Background Malaria in pregnancy remains a major public health problem in Africa and Ghana and has been associated with a variety of pregnancy-related adverse complications. The development of effective and timely health policies for the prevention and control of malaria and anemia in pregnancy; requires current and consistent data on the prevalence and risk factors. We report the prevalence and risk factors of malaria and anemia from three major hospitals across three regions in Ghana. Methods This multicenter cross-sectional study comprising a total of 628 pregnant women was conducted at the antenatal care units of the Achimota Hospital in the Greater Accra Region (n = 199), St. Michael's Hospital in the Ashanti Region (n = 221), and Effia Nkwanta Regional Hospital in the Western Region (n = 211). Questionnaires were administered to obtain socio-demographic, obstetrics and clinical data. Venous blood, stool and urine samples were collected for hematological profile and parasite identification using microscopy. Risk factors were evaluated using logistic regression models. Results The overall prevalence of P. falciparum malaria was 8.9%. Factors independently associated with malaria were self-reported mosquito exposure (moderate exposure: aOR = 3.11, 95% CI (1.12-8.61) and severe exposure: aOR = 10.46, 95% CI (3.86-28.34)) and non-use mosquito repellents (aOR = 3.29, 95% CI (1.70-6.39)). Multiparty (parity of 2: aOR = 0.19, 95% CI (0.05-0.70) and parity �3: aOR = 0.11, 95% CI (0.03-0.45)) and age (20-30 years old: aOR = 0.22, 95% CI (0.09-0.56)) reduced the odds of infection. The overall prevalence