Background: Despite the instrumental role of vaccines, public confidence is declining, and anti-vaccine movements have increased worldwide. With the goal of informing policy decisions and the development of interventions, we explore the concerns and challenges related to vaccine uptake (of childhood, maternal, and COVID-19 vaccines) among parents or caregivers of under-two children and pregnant women in urban and rural communities in the Philippines. Methods: Between May and June 2022, we conducted combined in-person and online interviews with purposively selected caregivers and pregnant women in the Calabarzon region (Naic, Cavite and Tanay, Rizal), and National Capital Region (Pasay and Muntinlupa Cities), Philippines. A total of 43 interviews were completed, audio-recorded, transcribed, and analyzed according to the tenets of hermeneutic phenomenology. Results: Our results, grounded on the social ecological model, underlined the interplays of contextual or logistical challenges on vaccine uptake, respondents' overarching concerns about vaccines, and their informational needs that affected their vaccine decision-making. Respondents described that the long-established maternal and childhood vaccines no longer represent a high-risk concern but highlighted their fears and hesitancy particularly to newer vaccines. Conclusion: Our findings underscore the multilayered challenges in vaccine decision-making among caregivers and pregnant women. The volatility of vaccine decision-making necessitates rethinking the current immunization process, recalibrating the health workforce, and reinvigorating the health information delivery channels for more inclusive and responsive health care.