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Effective and safe COVID-19 vaccines have been developed at a rapid and unprecedented pace to control the spread of the virus, and prevent hospitalisations and deaths. However, COVID-19 vaccine uptake is challenged by vaccine hesitancy and anti-vaccination sentiments, a global shortage of vaccine supply, and inequitable vaccine distribution especially among low- and middle-income countries including the Philippines. In this paper, we explored vaccination narratives and challenges experienced and observed by Filipinos during the early vaccination period. We interviewed 35 individuals from a subsample of 1,599 survey respondents 18 years and older in the Philippines. The interviews were conducted in Filipino, Cebuano, and/or English via online platforms such as Zoom or via phone call. All interviews were recorded, transcribed verbatim, translated, and analysed using inductive content analysis. To highlight the complex reasons for delaying and/or refusing COVID-19 vaccines, we embedded our findings within the social ecological model. Our analysis showed that individual perceptions play a major role in the decision to vaccinate. Such perceptions are shaped by exposure to (mis)information amplified by the media, the community, and the health system. Social networks may either positively or negatively impact vaccination uptake, depending on their views on vaccines. Political issues contribute to vaccine brand hesitancy, resulting in vaccination delays and refusals. Perceptions about the inefficiency and inflexibility of the system also create additional barriers to the vaccine rollout in the country, especially among vulnerable and marginalised groups. Recognising and addressing concerns at all levels are needed to improve COVID-19 vaccination uptake and reach. Strengthening health literacy is a critical tool to combat misinformation that undermines vaccine confidence. Vaccination systems must also consider the needs of marginalised and vulnerable groups to ensure their access to vaccines. In all these efforts to improve vaccine uptake, governments will need to engage with communities to ‘co-create’ solutions.