Despite the importance of integrated crop–livestock production in sustainable agricultural production and food security, there is a limited literature on the factors that influence this farming system’s efficiency. The objective of this study is to identify the sources and drivers of crop–livestock production efficiency for smallholder farmers in Ghana. First, a Färe–Primont index approach was applied to estimate and decompose overall efficiency (i.e. total factor productivity efficiency [TFPE]) of farmers into three components: technical efficiency (OTE), scale efficiency (OSE) and mix efficiency (OME). The results show that OME was the primary source of TFPE, followed by OTE and OSE. Second, the effects of various socioeconomic and management factors on the three efficiency components were investigated using a fractional regression model (FRM). Land ownership, extension, household head age, crop–livestock diversification and distance to markets improved crop-livestock farming system’s efficiency. However, the results show that these variables had different effects on the various efficiency components. For example, extension improved scale and mix efficiency but not technical efficiency. As a result, policies and development interventions must take these factors and their varying effects into account in order to improve crop-livestock farming system’s efficiency and smallholder farmers’ food security. Overall, this study emphasises the importance of employing methods that decompose efficiency into finer components and investigates their drivers.