The enforcement of the coronavirus disease 2019 (COVID-19) pandemic restrictions disrupted the traditional face-to-face qualitative data collection in public health. The pandemic forced qualitative researchers to transition to remote methods of data collection such as digital storytelling. Currently, there is a limited understanding of ethical and methodological challenges in digital storytelling. We, therefore, reflect on the challenges and solutions for implementing a digital storytelling project on self-care at a South African university during the COVID-19 pandemic. Guided by Salmon’s Qualitative e-Research Framework, reflective journals were used in a digital storytelling project between March and June 2022. We documented the challenges of online recruitment, obtaining informed consent virtually, and collecting data using digital storytelling as well as the efforts of overcoming the challenges. Our reflections identified major challenges, namely online recruitment and informed consent compromised by asynchronous communication; participants’ limited research knowledge; participants’ privacy and confidentiality concerns; poor internet connectivity; quality of digital stories; devices with a shortage of storage space; participants’ limited technological skills; and time commitment required to create digital stories. Strategies adopted to address these challenges included an ongoing informed consent process; flexible timelines for the creation of digital stories; one-on-one guidance on creating digital stories; and multiple online platforms to share digital stories. Our critical reflection offers practical guidance for the ethical conduct of digital storytelling in public health research and makes a significant contribution to methodological considerations for use in future pandemics. These ethical and methodological challenges should be recognized as features of the context of the research setting including restrictions imposed by the COVID-19 pandemic than disadvantages of digital storytelling.