Urgent changes in our food choices are needed for more sustainable, resilient and equitable food systems. Australian native plant-based foods have both environmental and health benefits. Including these foods in our diet may reduce both the risk of chronic diseases and the impact of climate change. This study explored the perceptions and attitudes towards food choices, sustainability and Australian native plant-based food among university students. (2) Methods: A cross-sectional online survey was completed by 212 university students in Australia from October to December 2022. Questions included information about sociodemographic characteristics, food choices, Australian native foods and the impact on sustainability. Logistic regression was used for analyses. (3) Results: Most participants recognised the impact of food choices on sustainability. There was a significant association between recognition of the impact of food choices on sustainability and the environmental and nutritional benefits of Australian native foods (OR = 2.89, 95% CI 1.29, 6.46, p = 0.010). Students who were familiar with or had tried Australian native plant-based foods were significantly more likely to recognise their environmental and nutritional benefits. (4) Conclusions: Students who recognise the impact of food choices on sustainability and the benefits of Australian native foods are more likely to include native foods in their diet. More studies are needed to investigate the specific native foods consumed and the barriers and facilitators to the intake of these foods.