Rice farming systems (RFSs) in southern Mozambique are very heterogeneous and diversified, which has implications for smallholders’ adoption of each RFS, as well as on rice production and productivity in the region. In this regard, it is important to understand: (i) which RFS typologies can be leveraged to improve rice production and productivity; (ii) the drivers for smallholder farmers’ decisions to adopt an RFS; and (iii) which policies/incentives could enhance existing RFSs. The present study was based on surveys of 341 smallholder rice farmers in the Chókwè Irrigation Scheme (CIS), southern Mozambique. Data on the productivity of rice, size of the herd, and total other crop types were used to frame the RFS typologies. A multinomial logit model (MLM) and multiple linear regression (MLR) were applied to determine the driver for each RFS, and predict the constraints for production and yield. Based on cluster analysis, four typologies of RFSs were identified: the subsistence farming system (FS), specialised rice FS, mixed crops FS, and rice–livestock FS. Farms with longer experience reported applying more fertiliser and seedlings per unit hectare. The availability of labour increased the likelihood of adopting the mixed crops FS and rice–livestock FS. Older households were more likely to adopt the subsistence FS, and live closer to the farming fields. Yield of rice was positively associated with inputs such as fertilisers, pesticides, and seedlings, as well as years of experience of the household. Our results suggest that smallholder farmers need more assistance and technical support to identify and adopt more productive and less costly RFSs in this region.