Information Systems (IS) diffusion in small and medium enterprises (SMEs) depends on various levels of networked, localised, and evolving determinants, such as the ones related to the adopter organisations, decision-takers, technologies, buyers, professional groups, higher education institutions, complementary innovations, and government policies. This complex view of IS implies the use of different disciplines and methodologies to study the diffusion process. The objective of this empirical research is to demonstrate how the philosophical stance of critical realism (CR) and the systems of innovation approach (SIA) for organising research are compatible, and address the multidisciplinarity and methodological pluralism required to move on the research of complex IS and recommend meaningful actions to practice. To exemplify our arguments we focus the study on one relevant determinant that affect the diffusion of IS in SMEs, namely public programmes.