While cholera imposes a substantial burden across the Democratic Republic of the Congo, its transmission dynamics vary by geography, socio-economic context or population habits. We investigated risk factors associated with laboratory-confirmed cholera among suspected cases in urban Goma and rural Bukama sites, across 2021-2022. Mixed-effects logistic regression models were fitted independently by site. Positivity rates were higher in Goma (70.2%, 1688/2405) than in Bukama (49.4%, 390/790). In both sites, rainy seasons increased odds of testing positive (OR=3.89, 95%CI [2.93-5.16] and 2.00 [1.39-2.86] for Goma and Bukama, respectively) while receiving [≥]1 Oral Cholera Vaccine dose was protective (0.53 [0.37-0.74] and 0.58 [0.37-0.91]). Some risk factors were significant only in Goma, including displacement status (1.93 [1.11-3.35]), household cholera case exposure (1.79 [1.31-2.45]), consumption of surface water (2.11 (1.46-3.03]) or from water tankers (1.75 (1.24-2.47]). This study shows that cholera risk factors vary across endemic settings, giving insights for improved, locally-adapted control measures.