Food prices have escalated due to impacts of the COVID-19 pandemic on global food systems, and other regional shocks and stressors including climate change and war. Few studies have applied a health lens to identify the most affected foods. This study aimed to assess costs and affordability of habitual (unhealthy) diets and recommended (healthy, equitable and more sustainable) diets and their components in Greater Brisbane, Queensland, Australia from 2019 to 2022 using the Healthy Diets Australian Standardised Affordability and Pricing protocol. Affordability was determined for reference households at three levels of income: median, minimum wage, and welfare-dependent. The recommended diet cost increased 17.9%; mostly in the last year when the prices of healthy foods, such as fruit, vegetables and legumes, healthy fats/oils, grains, and meats/alternatives, increased by 12.8%. In contrast, the cost of the unhealthy foods and drinks in the habitual diet ‘only’ increased 9.0% from 2019 to 2022, and 7.0% from 2021 to 2022. An exception was the cost of unhealthy take-away foods which increased by 14.7% over 2019–2022. With government COVID-19-related payments, for the first time recommended diets were affordable for all and food security and diets improved in 2020. However, the special payments were withdrawn in 2021, and recommended diets became 11.5% less affordable. Permanently increasing welfare support and providing an adequate minimum wage, while keeping basic, healthy foods GST-free and increasing GST to 20% on unhealthy foods, would improve food security and diet-related health inequities. Development of a Consumer Price Index specifically for healthy food would help highlight health risks during economic downturns.