The onset of this new pandemic has highlighted the numerous critical issues at the organizational level, which involve both national healthcare and the judicial system. For this reason, nurses working in prisons may exhibit a poor quality of life, mainly related to their high level of work stress. This cross-sectional survey aimed to assess the emotional state of nurses working in the Judicial Psychiatry Hospital of Barcellona PG (Messina, Italy) during the COVID-19 pandemic. Data collection occurred twice: from 1 April to 20 May 2020 (i.e., during the Italian lockdown) and from 15 October to 31 December 2021 (during the second wave). At baseline, the 35 enrolled nurses presented medium to high levels of stress. At T1, they had a reduction in perceived personal achievement (MBI-PR p = 0.01), an increase in emotional exhaustion (MBI-EE p < 0.001), and stress (PSS p = 0.03), as well as anxiety (STAI Y1/Y2 p < 0.001). Most participants underlined the high usability of the online system (SUS: 69.50/SD 19.9). We also found increased stress, anxiety, and burnout risk in nursing staff. The study clearly demonstrates that the first year of the COVID-19 pandemic in Italy caused a worsening of mental health among nurses working in prisons. We believe that monitoring the mental state of healthcare professionals is fundamental to improving their quality of life and healthcare services.