Background and Objectives: The coronavirus disease 2019 (COVID-19) pandemic originated in Wuhan, China, in December 2019, the first case diagnosed since January 2020 in Taiwan. The study about the potential impact of the COVID-19 pandemic on event, location, food source, and pathogens of foodborne disease (FBD) is limited in Taiwan. Our aim in this study is to investigate FBD in the context of the COVID-19 pandemic. Materials and Methods: We collected publicly available annual summary data from the FBD dataset in the Taiwan Food and Drug Administration and Certifiable Disease on reported FBD in Taiwan from 2019 to 2020. We used logistic regression to evaluate changes in the occurrence or likelihood of FBD cases and Poisson regression to examine the relative risk (RR) between FBD and climate factors. Results: Similar events occurred in 2019 and 2020, but the total number of FBD cases decreased from 6935 in 2019 to 4920 in 2020. The places where FBD decreased were in schools, hospitals, outdoors, vendors, and exteriors. The top place in FBD shifted from schools to restaurants. The top food source for FBD has changed from boxed food to compound food. Bacillus cereus and Salmonella emerged as the top two observed bacterial pathogens causing FBD. The risk of FBD cases increased with a higher air temperature, with an RR of 1.055 (1.05–1.061, p < 0.001) every 1 °C. Conclusion: The incidence of FBD decreased significantly during the COVID-19 pandemic in Taiwan. This decline may be attributed to protective measures implemented to control the spread of the virus. This shift in locations could be influenced by changes in public behavior, regulations, or other external factors. The study emphasizes the importance of understanding the sources and effectiveness of severe infection prevention policies. The government can use these findings to formulate evidence-based policies aimed at reducing FBD cases and promoting public health. Consumers can reduce the risk of FBD by following safe food handling and preparation recommendations.