The COVID-19 pandemic rapidly led to changes in the mode of teaching, learning and assessments in most tertiary institutions worldwide. Notably, non-invigilated summative assessments became predominant. These changes heightened anxiety and depression, especially among individuals with less resilient coping mechanism. We explored the perceptions and experiences of mental health difficulties of students in tertiary education regarding non-invigilated alternative assessments in comparison to invigilated assessments. A pragmatic, mixed method cross sectional design was conducted online via Qualtrics. Thematic analysis of text was carried out using NVivo 12. In the quantitative analysis, univariable and multivariable ordinal logistic models were used to examine the potential factors for preference among students in higher education. A total of 380 Nursing and Social Science students responded to the survey. Approximately 77% of students perceived non-invigilated assessments to be less stressful compared to invigilated exams. Age, course of study, stage of studies, and number of units enrolled per semester were identified as significant drivers for students’ perceived preference for non-invigilated assessments. There was an inverse relationship between the perception of stress associated with invigilated exams and the age of students. For instance, students aged between 18-24 were 5 times more likely to prefer non-invigilated exams compared to those aged 55 or more. Comparatively, students in early stages of studies had higher preference for non-invigilated assessments. However, there was a preference reversal for students enrolled in 2 or less units per semester. Social sciences students were two times more likely to prefer non-invigilated examinations to invigilated examinations compared to nursing students. The findings reinforce the use of alternative assessments in higher education as a mitigating agency to lessen the mental health burden of tertiary students in post COVID-19 era.