Objective: Evidence suggests that young adults (aged 18–34) were disproportionately impacted by the COVID-19 pandemic, but little is known about their longer-term mental health changes beyond the early pandemic period. This article investigates heterogeneous trajectories of mental health among Australian young adults across 2 years of the pandemic and identifies a broad range of associated risk and protective factors. Method: Young adults ( N = 653, M_age = 27.8 years) from the longitudinal Alone Together Study were surveyed biannually between July 2020 and June 2022. Measures assessed anxiety (7-item Generalised Anxiety Disorder scale) and depression (9-item Patient Health Questionnaire) symptoms at Waves 1–4, as well as demographic, psychological, adversity and COVID-19 factors at baseline. Results: Four and three distinct trajectories of anxiety and depressive symptoms, respectively, were identified through growth mixture modelling. The proportion of participants in each anxiety trajectory were Asymptomatic (45.9%), Mild Stable (17.9%), Moderate–Severe Stable (31.1%) and Initially Severe/Recovering (5.1%). For depression, Mild Stable (58.3%), Moderate–Severe Stable (30.5%) and Reactive/Recovering (11.2%). Baseline factors associated with severe symptom trajectories included a lifetime mental health disorder, pre-pandemic stressful events, identifying as LGBTQIA+ and/or female, and experiencing one or more infection-control measures. Higher household income was protective. Conclusion: Most young adults demonstrated stable trajectories of low or high symptoms during the pandemic, with smaller groups showing initially severe or reactive symptoms followed by marked improvements over time. Vulnerable subgroups (gender- or sexuality-diverse, those with prior adversity or pre-existing mental ill-health) may face ongoing impacts and require targeted psychosocial supports to assist their mental health recovery post-COVID-19 and in the event of future crises.