COVID-19 was responsible for more than 7 million deaths globally, as well as numerous morbidities and social and economic effects. While COVID-19 vaccines were seen as a marvel of science by the scientific community, much of the public had concerns related to COVID-19 vaccines, with certain groups—such as pregnant and lactating women—having specific concerns related to vaccine effects on their pregnancy and breast milk. In this qualitative study, we interviewed stakeholders in Bangladesh (n = 26) and Kenya (n = 94) who affect the decision-making process related to COVID-19 vaccine acceptance among pregnant and lactating women. These included pregnant and lactating women themselves, community gatekeepers or family members, healthcare workers, and policymakers. Several themes related to confidence and vaccine preference emerged. Stakeholders indicated a lack of confidence related to non-mRNA vaccines due to safety concerns, number of doses, and media coverage; lack of confidence related to mRNA vaccines due to safety concerns; and preference for non-mRNA vaccines due to health system compatibility and availability. While COVID-19 vaccine availability in much of the world—particularly in low-and middle-income countries—affected the public’s ability to have a choice in the vaccine they received, there were evident vaccine preferences. As the public health world will continue to face other infectious disease outbreaks, bolstering vaccine confidence broadly and specifically related to new technologies will be paramount to realize the individual-and population-level benefits of life-saving vaccines.