Indigenous peoples in Peninsular Malaysia, known as Orang Asli, have been associated with the problem of malnutrition. Approximately 40% of their children are underweight. Indigenous peoples' distinct social, cultural, and economic traits, which differ from those of the dominant communities in which they live, may pose significant challenges for health care providers (HCPs) in addressing the malnutrition issue. This study explores challenges encountered by HCPs, with at least six months of experience in monitoring the growth parameters of Orang Asli children residing in Perak State in Peninsular Malaysia. A cross-sectional study was conducted between December 2020 and June 2021, involving three focus group discussions and three in-depth interviews. Thematic analysis was used. A total of 19 participants (6 nurses, 5 nursing managers, 4 medical officers, 2 nutritionists, a family medicine specialist, and a paediatrician) took part in this study. The challenges were summarized into four themes: (I) accessibility to nutrition, (II) accessibility to healthcare services, (II) skills of HCPs, and (IV) challenges of implementing nutrition programs. The inability of the Orang Asli children to access nutritious food was due to poverty, different perceptions of life priorities, and the practice of food taboos among the communities. Inadequate infrastructure and transportation discourage parents from bringing their children to healthcare facilities. The belief in and preference for traditional healing, the practice of semi-nomadic lifestyles, and fear of HCPs and their timid nature were factors that prevented Orang Asli children from accessing healthcare services. HCPs need to equip themselves with cross-cultural communication and interaction skills and adapt their skills to environmental challenges to overcome unexpected encounters in mobile clinics. The non-exposed food items, the risk of food basket sharing with other family members, and community feeding programs' coordination were the challenges to be addressed when implementing nutrition programmes for Orang Asli children. The challenges of HCPs are multifactorial and require a multifaceted approach. There is a need for joint efforts of stakeholders, from communities and non-governmental organisations (NGOs) to the health authorities, to address the challenges of HCPs.