Background For Malaysia, a nation highly dependent on migrant labour, the large non-citizen workforce presents a unique health system challenge. Although documented migrant workers are covered by mandatory healthcare insurance (SPIKPA), financial constraints remain a major barrier for non-citizen healthcare access. Malaysia recently extended protection for migrant workers under the national social security scheme (SOCSO), previously exclusive to citizens. This study aims to evaluate healthcare financing and social security policies for migrant workers to identify policy gaps and opportunities for intervention. Methods A total of 37 in-depth interviews were conducted of 44 stakeholders from July 2018 to July 2019. A mixed-methods analysis combining major themes from qualitative interviews with policy document reviews was conducted. Descriptive analysis of publicly available secondary data, namely revenues collected at government healthcare facilities, was conducted to contextualise the policy review and qualitative findings. Results We found that migrant workers and employers were unaware of SPIKPA enrolment and entitlements. Higher fees for non-citizens result in delayed care-seeking. While the Malaysian government nearly doubled non-citizen healthcare fees revenues from RM 104 to 182 million (USD 26 to 45 million) between 2014 to 2018, outstanding revenues tripled from RM 16 to 50 million (USD 4 to 12 million) in the same period. SPIKPA coverage is likely inadequate in providing financial risk protection to migrant workers, especially with increased non-citizens fees at public hospitals. Undocumented workers and other migrant populations excluded from SPIKPA contribution to unpaid fees revenues are unknown. Problems described with the previous Foreign Workers Compensation Scheme (FWCS), could be partially addressed by SOCSO, in theory. Nevertheless, questions remain on the feasibility of implementing elements of SOCSO, such as recurring payments to workers and next-of-kin overseas. Conclusion Malaysia is moving towards migrant inclusion with the provision of SOCSO for documented migrant workers, but more needs to be done. Here we suggest the expansion of the SPIKPA insurance scheme to include all migrant populations, while broadening its scope towards more comprehensive coverage, including essential primary care.