Evaluating e-learning acceptance at the universities in Iran during the COVID-19 pandemic was conducted to discover the challenges and students' preferences. During the lockdown, virtual classes run in Iran by using online platforms based on universities' facilities. The importance of online education led to form the framework of this quantitative study based on the Technology Acceptance Model (TAM) and external factors including perceived resources, subjective norms, and COVID-19 stress. The Partial Least Squares (PLS) was used to analyze data. To generate a consistent model and reliable results, 136 students were the sample size which was identified based on the exact calculations for PLS sampling. The questionnaire which was prepared in Google Drive was distributed through the online universities' groups. The results disclosed that perceived ease of use was a strong predictor of perceived usefulness. Both perceived usefulness and perceived ease of use displayed a significant role as a predictor of attitude. Behavioral intention to use was influenced meaningfully by attitude and subjective norms. The effect of behavioral intention on online system usage was proved, on the contrary, the influence of COVID-19 stress on online system usage was not confirmed. It is hoped that a standard scale would be introduced by future psychological studies to fill the lack of information about COVID-19's mental facets. This study confirmed the significant effects of e-learning challenges on students' behavior toward using online systems. Future research might explore each university platform separately in order to offer suitable solutions based on each university's needs.