Purpose - The purpose of this paper is to explore the effects of inter-organisational compatibility on inter-organisational information systems (IOIS) integration and supply chain performance of large enterprises (LE) and small-medium enterprises (SMEs) in Australian retailing chains. Design/methodology/approach - Convergent interviewing technique was used to collect data from managers of 12 fast-moving consumer goods and hardware manufacturing and retailing organisations. Within- and cross-case analyses were used to analyse the data. Findings - The results indicate that technical, strategic and cultural compatibility between supply chain partners are antecedents to IOIS integration and supply chain performance of both LE and SMEs. A conceptual model explaining the relationship between inter-organisational compatibility, IOIS integration and supply chain performance is advanced. The study extends congruency theory to information systems and supply chain contexts. Practical implications - The study provides some guidelines to supply chain and information systems managers on how inter-organisational compatibility can be used to facilitate IOIS integration and enhance supply chain performance in both large and small firms. Technical, strategic and cultural compatibility emerged as antecedents to IOIS integration, suggesting the need for supply chain managers especially within SMEs to pay close attention to inter-organisational compatibility factors when integrating IOIS with supply chain partners. Originality/value - Research relating IOIS integration and supply chain is limited, especially in the SMEs context. Thus, this paper contributes to the body of knowledge by examining how inter-organisational compatibility influences organisations decisions to integrate IOIS with supply chain partners using congruency theory.