COVID-19 booster vaccination has shown to add to the protection against infection with SARS-CoV2 and subsequent severe disease. This longitudinal cross-border study aimed to identify factors associated with COVID-19 booster vaccine intentions in an initially vaccinated adult population living in the Meuse-Rhine Euroregion (EMR; including the Netherlands, Belgium, and Germany) and differences between countries. Data collection took place in autumn of 2021 and consisted of online questionnaires sent to a random sample of the population based on governmental registries. Data from 3,319 fully and partially vaccinated adults were used to examine determinants of non-positive intention for a booster vaccination (i.e., uncertain or do not want), using multivariable logistic regression analyses weighted by age group, sex, and country. Compared to German residents, Dutch residents (OR = 2.4) and Belgian residents (OR = 1.4) were more likely to be uncertain or not want to receive a booster vaccine in September-October 2021. Factors independently associated with non-positive intention were female sex (OR = 1.6), absence of comorbidities (OR = 1.3), time since last vaccination less than 3 months ago for those fully vaccinated (OR = 1.6), being partially vaccinated (OR = 3.6), a negative experience with communication of COVID-19 measures (OR = 2.2), and regarding measures as ineffective (OR = 1.1). Results indicate that booster vaccine intentions differ between countries in the cross border Meuse-Rhine Euroregion. Non-positive intention for the booster vaccine is prevalent in all three countries of the EMR, but to a different extent, as shown in this study. Cross-border collaboration and sharing information and knowledge about vaccination strategies could play a role in limiting the impact of COVID-19.