Access to inclusive sanitation for people with disabilities (PWDs) remains a global challenge, including in Indonesia, where 10–15% of its population is disabled. Inclusive sanitation facilities can be achieved when PWDs are involved in the sanitation-related decision-making process, e.g., designing toilet that meets their needs. This study aims to investigate the situation of the sanitation facility in houses of PWDs and understand knowledge, attitude, and practices related to PWD participation in sanitation programs using a case study in two provinces in Indonesia: Nusa Tenggara Barat and Nusa Tenggara Timur. Quantitative data were taken from 129 PWD households, and qualitative data were from in-depth interviews with relevant stakeholders. The latter was presented in a causal loop diagram. Less than 5% had inclusive sanitation at home, mainly due to no supportive tools and bins. The knowledge levels related to sanitation and PWDs participation in sanitation programs were relatively low. Economic condition was one of the barriers for PWDs to participate in the sanitation program. Statistical analysis found that a higher household head education level was associated with a more positive attitude and higher PWD participation in sanitation programs. Although Indonesian law supports PWD participation, the implementation remains a challenge. This study also underlines the need for capacity building in facilitating PWDs’ involvement in sanitation programs and community meetings. Finally, barriers to PWD participation can come from different levels and actors, e.g., the family, the community, the district level, and the PWD itself, indicating the need to involve actors at all levels to enhance PWD participation in the sanitation program that leads to inclusive sanitation facilities for all groups.