Improving the historically low reproductive performance of beef cattle in smallholder systems is essential for its productivity and profitability. Therefore, identifying and addressing risk factors associated with low performance in this system present an opportunity for improvement. The study aimed to evaluate the effect of animal and management risk factors on pregnancy rate (PR), fetal and calf loss (FC), calving interval (CI) and days open (DO) in smallholder beef cattle farms. A multi-stage selection approach was conducted in five provinces of South Africa. Cow records (3694) collected from 40 smallholder herds over two years (2018–2019) were analysed. Data on animal and herd management factors including body condition score (BCS), cow age class, breed type, lactation status, culling old/non-productive cows, record-keeping, and breeding and calving seasons were recorded. The GLIMMIX procedure was computed to determine risk factors associated with performance indicators (PR, FC, CI and DO). Risk factors highly associated with performance were breed type, BCS, cow-age class and breeding/calving season (P ≤ 0.05). Indicators FC, DO and CI increased with decreased BCS, autumn calving seasons, and in first calvers and aged cows. Whereas, PR increased with increasing odds of BCS and breeding seasons between December-March, November-February and January-March. Optimizing reproductive performance in smallholder beef cattle herds may involve managing cow body condition, breeding with adapted genotypes and synchronizing breeding with favourable seasons. Therefore, record keeping and regular monitoring of herd nutrition, climate and breed performance may be significant in improving reproductive performance in smallholder herds.