This study examined the implementation of the Bureau of Jail Management and Penology (BJMP) treatment policies for Persons Deprived of Liberty (PDL) with special needs, focusing on lesbian, gay, bisexual, transgender, queer, and intersex (LGBTQI) individuals, senior citizens, and persons with disabilities (PWD). It aimed to assess compliance with treatment policies, identify challenges, examine differences in perceptions between jail officers and PDL, and propose strategies to enhance policy implementation. A mixed-methods design was used, with 160 respondents comprising 120 PDL and 40 jail officers from selected BJMP facilities. Eight key informants joined the qualitative phase. Quantitative data were statistically analyzed, while qualitative data underwent Braun and Clarke’s six-step thematic analysis. Results showed a generally high level of compliance across four areas: admission and classification; housing and segregation; welfare and development programs; and safety and security. However, significant differences were found between Jail Officers and PDL with disabilities in their perceptions of policy implementation. Key challenges identified were overcrowding, inadequate healthcare services, lack of specialized training for personnel, and unequal access to programs. The study concluded that while BJMP has comprehensive policies, resource gaps and operational limitations hinder consistent implementation, highlighting the need to bridge policy and practice to ensure humane and rehabilitative jail management.