Reaching out to the poor and the informal sector is a major challenge for achieving universal coverage in lesser-developed countries. In Cambodia, extensive coverage by health equity funds for the poor has created the opportunity to consolidate various non-government health financing schemes under the government's proposed social health protection structure. This paper identifies the main policy and operational challenges to strengthening existing arrangements for the poor and the informal sector, and considers policy options to address these barriers. Conducted in conjunction with the Cambodian Ministry of Health in 2011-12, the study reviewed policy documents and collected qualitative data through 18 semi-structured key informant interviews with government, non-government and donor officials. Data were analysed using the Organizational Assessment for Improving and Strengthening Health Financing conceptual framework. We found that a significant shortfall related to institutional, organisational and health financing issues resulted in fragmentation and constrained the implementation of social health protection schemes, including health equity funds, community-based health insurance, vouchers and others. Key documents proposed the establishment of a national structure for the unification of the informal-sector schemes but left unresolved issues related to structure, institutional capacity and the third-party status of the national agency. This study adds to the evidence base on appropriate and effective institutional and organizational arrangements for social health protection in the informal sector in developing countries. Among the key lessons are: the need to expand the fiscal space for health care; a commitment to equity; specific measures to protect the poor; building national capacity for administration of universal coverage; and working within the specific national context.