Background: Mobile phone-based tools are increasingly used to collect data on non-communicable disease (NCD) risk factors, particularly in low-resource settings where traditional data collection systems face operational and infrastructural constraints. This study examined stakeholder perspectives on the use of enhanced mobile phone-based capabilities to support the collection of public health surveillance data on NCD risk factors in low-resource settings. Methods: An exploratory qualitative study was conducted between November 2022 and July 2023. Twenty in-depth interviews were conducted with public health specialists, ethicists, NCD researchers, health informaticians, and policy makers in Uganda. Thematic analysis was used to interpret the results. Results: Four themes emerged from the data, including benefits of using mobile phone capabilities for NCD risk factor data collection; ethical, legal, and social implications; perceived challenges of using such mobile phone capabilities; and proposed solutions to improve the utility of phone-based capabilities in data collection on NCD risk factors. Participants recognized the potential of mobile technologies to improve data collection efficiency and expand access to hard-to-reach populations. However, concerns emerged regarding inadequate informed consent, risks to privacy and confidentiality, unclear data ownership, and vulnerabilities created by inconsistent enforcement of data protection laws. Social concerns included low digital literacy, unequal access to mobile devices, and fear of stigmatization. Participants emphasized the need for transparent communication, robust data governance, and community engagement. Conclusion: Mobile phone-based systems can strengthen the collection of NCD risk factor data in low-resource settings; however, their benefits depend on addressing key ethical, legal, and social challenges. To ensure responsible deployment, digital health initiatives must prioritize participant autonomy, data protection, equity, and trust building. Integrating contextualized ethical, legal, and social considerations into design and policy frameworks will be essential to leveraging mobile technologies in ways that support inclusive and effective NCD prevention and control.