Background: Globally, vulnerable populations have been disproportionately affected by the COVID-19 pandemic and subsequent responses, such as lockdown measures and mass vaccinations. Numerous ethical challenges have arisen at different levels, be it at the policy-making level or on the ground. For example, policymakers have to contain a highly contagious disease with high morbidity using scarce resources, while minimizing the medium- to long-term social and economic impacts induced by containment measures. This study explores the impact of COVID-19 on vulnerable populations in Malaysia by using an intersectional framework that accounts for overlapping forms of marginalization. Methods: This study utilizes in-depth qualitative data obtained from 34 individuals and organizations to understand the impact of the COVID-19 outbreak on vulnerable populations in Malaysia. We utilize four principles of ethics to guide our coding and interpretation of the data - namely beneficence, non-maleficence, justice and autonomy. We utilize a frequency analysis to roughly understand the types of ethical issues that emerged. Using hermeneutic content analysis (HCA), we then explore how the principles interact with each other. Results: Through the frequently analysis, we found that although beneficence was very prevalent in our dataset, so was a significant amount of harm - as perpetuated through injustice, the removal or lack of autonomy and maleficence. We also unearthed a worrying landscape of harm and deep systemic issues associated with a lack of support for vulnerable households - further exacerbated during the pandemic. Conclusions: Policy recommendations for aid organizations and society to mitigate these ethical problems are presented, such as long overdue institutional reforms and stronger ethical practices rooted in human rights principles, which government agencies and aid providers can then use in the provision of aid to vulnerable populations.