The severity of both the COVID-19 clinical picture and confinement measures in Slovenia was higher during the initial phase of the pandemic in 2020 than during the Omicron wave in 2022. This could lead us to expect a higher level of distress during the initial phase. On the other hand, prolonged stress can have a detrimental effect on mental health. This study aimed to explore how the prolonged stress of the COVID-19 pandemic and the accompanying changes affected the mental health of young adults in Slovenia. We analyzed and compared the levels of depression, anxiety, stress, and suicidal ideation in young adults during the initial phase of the pandemic and the Omicron wave, as well as between the COVID-19-infected and non-infected individuals. An online survey was used to survey 587 young adults in the first wave (July-December 2020) and 511 in the Omicron wave (January-February 2022). Levels of depression, anxiety, stress, and suicidal ideation were compared using Mann-Whitney U test. Results show that the Omicron wave significantly worsened depression, anxiety, stress, and suicidal ideation. Young adults who had tested positive for COVID-19 reported no worse or only slightly worse mental health than those who never tested positive. The current study provides new evidence about the mental health of young adults during the Omicron wave. Our results show that two years into the pandemic, they expressed more negative emotions and suicidal thoughts than at the beginning.