Objectives Pregnancy carries a high risk for millions of women and varies by urban–rural location in Nigeria, a country with the second highest maternal deaths in the world. Addressing multilevel predictors of poor pregnancy outcomes among antenatal care (ANC) attendees in primary health care (PHC) facilities could reduce the high maternal mortality rate in Nigeria. This study utilised the “Risk Approach” strategy to (1) compare the risks of poor pregnancy outcomes among ANC attendees by urban–rural location; and (2) determine predictors of poor pregnancy outcomes among ANC attendees in urban–rural PHC facilities in Cross River State, Nigeria. Methods A cross-sectional survey was conducted in 2011 among 400 ANC attendees aged 15–49 years recruited through multistage sampling. Data on risk factors of poor pregnancy outcomes were collected using interviewer-administered questionnaires and clinic records. Respondents were categorised into low, medium or high risk of poor pregnancy outcomes, based on their overall risk scores. Predictors of poor pregnancy outcomes were determined by multilevel ordinal logistic regression. Results A greater proportion of the women in the rural areas were below the middle socio-economic quintile (75 vs. 4 %, p < 0.001), had no education (12 vs. 2 %, p < 0.001), and were in the 15–24 age group (58 vs. 35 %, p < 0.001) whereas women in the urban areas were older than 35 years (10 vs. 5 %, p < 0.001). The women attending antenatal care in the urban PHC facilities had a low overall risk of poor pregnancy outcomes than those in the rural facilities (64 vs. 50 %, p = 0.034). Pregnant women in the urban areas had decreased odds of being at high risk of poor pregnancy outcomes versus the combined medium and low risks compared with those in the rural areas (OR 0.55, 95 % CI 0.09–0.65). Conclusions for Practice Pregnant women attending antenatal care in rural PHC facilities are more at risk of poor pregnancy outcomes than those receiving care in the urban facilities. Health programmes that promote safe pregnancy should target pregnant women in rural settings.