The lockdown and social distancing policies to reduce COVID-19 spread and perceived safety threats of COVID-19 significantly affected people’s travel behavior. Greece has been suffering from the COVID-19 pandemic, and people’s mobility behavior has been greatly affected. This study aims at: (1) exploring the variations in individuals’ trip frequencies by mode and purpose before and after the COVID-19 outbreak; (2) understanding the effects of individual differences (i.e., sociodemographic details) and perceptions towards COVID-19 (i.e., the perceived threats of COVID-19) on people’s mobility behavior changes after the outbreak; (3) underlining the individuals’ perceptions of the COVID-19 threat on the willingness of public transportation usage. Overall, 403 responses were collected in late 2020. A series of random parameter Probit modeling results reveal multiple individual and perception factors affecting the changes in mobility behavior in Greece. The results from structural equation modeling indicate that perceived COVID-19 threats affect the attitudes and subjective norms towards people’s intentions to use public transportation. The results from this study provide valuable insights for transportation authorities to develop effective strategies to manage traffic during the spread of disease for a possible future epidemic.