Background: The COVID-19 pandemic may have inhibited the development of critical thinking and emotional intelligence of nursing students due to the transition from traditional to online learning environments. Objective: The objective was to evaluate the development of critical thinking, emotional intelligence, and the perceived learning environment of nursing students during the pandemic from their first to second year. Methods: This was a longitudinal study of 82 nursing students from 2 universities in Greece. We measured critical thinking disposition, emotional intelligence, and the students’ perceptions of the learning environment in 2 phases, separated by a 10 month interval, before and during the pandemic. Results: Students had moderate-to-high critical thinking and emotional intelligence and perceived the learning environment as more positive than negative in both phases. However, there were no statistically significant changes between phases in critical thinking disposition (mean score 44.3 vs 45.1, p = .224) and emotional intelligence (mean score 5.05 vs 5.06, p = .950) between the 2 phases. Nevertheless, students rated the online learning environment (phase 2) higher than the traditional (mean score 137.8 vs 132.2, p = .005). Conclusions: Critical thinking and emotional intelligence did not change, but students favored the online learning environment over the traditional. These findings suggest that nurse educators persevered, adapted, and maintained the quality of the learning environment despite the pandemic. Moreover, the utilization of an online learning environment may have led to enhanced enjoyment and engagement for students, which could potentially result in improved learning outcomes.