For decades, there has been significant investment in the development of agricultural technologies that aim to increase productivity of smallholder farmers in Africa. But farm output and productivity have stagnated and poverty rates have remained high and even increasing in some areas. At the same time, increases in human population levels have resulted in rising demand for food as well as for arable land. The growing intensification of farming has been accompanied by degradation of wild lands, including tropical forests and wetlands, at an alarming rate. Further pressure on fragile land has come from associated urbanization, leading to agricultural land being converted to residential and industrial uses with serious consequences for agricultural production and food supply. The recent increases in food prices across the globe as well as South Africa have drawn attention to this problem even more strongly. The main objective of the current study was to investigate farmer’s perception of the relative importance of crop-livestock integration in the small holder farming systems. Data were collected from 70 emerging and smallholder farmers selected by stratified random sampling in the communities surrounding Alice, Middledrift and the Seymour- Balfour area of Nkonkobe municipality of the Eastern Cape Province. To collect the data, a semi-structure questionnaire was administered to the respondents through face-to-face interviews. Descriptive statistics were used to characterize the farmers in terms of their socio-economic and demographic backgrounds. A series of multiple linear regression models and a binary logistic regression equation were fitted to determine the factors influencing farmers’ perception and how these in turn contribute to the decision to adopt or not to adopt crop-livestock integration. The results of the study reveal that small farmers in the Nkonkobe municipality have the possibility of realizing immense benefits from the integrated systems which also have the potential to lead to substantial improvements of the physical, chemical and biological soil properties. There is clear evidence of widespread interest to experiment with the practices based on the strong positive perceptions that a majority of the survey farmers exhibited during the course of the survey. But the farmers are facing challenges in coping with the associated complexities of competition on land, and management skill which are often in limited supply. That in most cases is not enough and efficient even to manage one of these two enterprises alone and reduction in crops yield due to use of manure as a substitute of fertilizer. Constraints to integrating crops and livestock include the competition for resources, especially land. Managing two types of farming on the same farm was perceived as difficult and many respondents held the view that use of waste of one enterprise as input to the other enterprise can reduce productivity. For example some farmers considered that the use of manure to improve soil fertility may not lead to output growth to the same extent as the use of fertilizer. A number of farmers (86%) pointed out that they only market their produce after deducting their consumption share, highlighting the crucial role of food security as a motivation for crop-livestock integration. Complementation of inputs rather than substituting inputs is required to render the system more productive and sustainable as costs are minimized and output is boosted. Associations of grain and livestock producers are useful for filling these gaps which include limited access to credit, technology and knowledge and can promote the adoption of a crop-livestock system.