We used data collected during the COVID-19 pandemic, from March to June 2021, to examine how Italian upper secondary schools reorganized their activities for remote learning (RL). We conducted a three-level survey, administering questionnaires to students (11th and 13th graders), teachers, and school principals at each institution. The final sample includes 11,154 students, 3,905 teachers, and 105 school principals. The data allow us to describe: a) how schools adjusted to the pandemic to ensure learning effectiveness during RL, b) how teachers and school principals managed the transition from traditional to online teaching, c) the perceptions of students, teachers, and school principals regarding the effectiveness of RL. This analysis highlights Italian schools’ challenges in changing teaching styles during RL and identifies inequality patterns at individual and school levels. It also underscores a significant gap between teachers’ perceptions of their digital skills and the actual use of ICT in class during RL activities. Our results identify a positive and robust relationship between the use of innovative teaching methodologies in class, the adoption of appropriate organizational innovations at the school level, and specific teachers’ training with the student’s perceptions of learning and other outcomes related to student success.