The emergence of the COVID-19 pandemic in 2020 led to many changes in people’s lifestyles and governments’ policies worldwide. In the education area, there has been an increase in the use of online learning due to the necessity of social distancing and an interruption in the transmission of information. The present study aimed to determine differences between online and in-person education systems regarding teachers’ perceptions of educational knowledge and pedagogical skills during the COVID-19 pandemic. In total, 1,500 teachers were selected from universities with in-person classes and 1,400 instructors were chosen from online universities in the cities of Tehran, Shiraz, Isfahan, Yazd, Tabriz, Ahvaz, Zanjan, and Arak, Iran, in 2022. Notably, the teachers were active in the fields of general and business English. Overall, a questionnaire including 30 items was applied, and each item scored teachers’ educational knowledge and pedagogical skills based on their perceptions using a 5-point Likert scale. Data analysis was performed using MANOVA. According to the results, there was a significant difference between online and in-person education systems regarding general English teachers’ perceptions of their educational knowledge and pedagogical skills. Similar results were obtained for business English teachers. In fact, general and business English teachers of in-person universities had a higher perception of their educational knowledge and pedagogical skills compared with teachers of online universities.