Background and Objectives: In response to the COVID-19 pandemic, Israel prioritized pregnant women for vaccination, recognizing them as a high-risk group. This study aims to explore factors influencing the acceptance of Influenza, Pertussis (T-dap), and COVID-19 vaccines among pregnant women, focusing on attitudes, social norms, perceived control, and risk perceptions. Additionally, the study compares acceptance patterns between traditional vaccines and the newer COVID-19 vaccine. Methods: A prospective cohort study was conducted between December 2019 and December 2021 involving 449 predominantly Israeli pregnant women. A survey was administered to gather data on demographics, obstetric history, vaccination history, and factors influencing vaccination decisions. Results: COVID-19 vaccine uptake was the highest at 64% (202/314), followed by T-dap at 49% (221/449) and Influenza at 32% (146/449). Multivariable logistic regression showed that non-religious women and those with academic education were more likely to accept vaccines, especially the COVID-19 vaccine. Physician recommendations were the most influential factor in vaccine acceptance, while internet and media sources played a significant role in shaping COVID-19 vaccine decisions. Perceived risks varied: Whooping Cough was seen as the greatest threat to newborns, while COVID-19 posed the highest risk to mothers. Analyzing maternal and neonatal disease perception using multivariable linear regression, we found that information on maternal and neonatal Flu, Whooping Cough, and COVID-19 was significantly positively correlated with disease perception for each condition. Conclusions: Healthcare providers play a crucial role in influencing vaccine decisions, especially through personalized communication. Strategies targeting religious communities and leveraging media can help address vaccine hesitancy, ultimately improving maternal and neonatal health outcomes.