Abstract Background Rapid simultaneous increases in ultra-processed food sales and obesity prevalence have been observed worldwide, including in Australia. Consumption of ultra-processed foods by the Australian population was previously shown to be systematically associated with increased risk of intakes of nutrients outside levels recommended for the prevention of obesity. This study aims to explore the association between ultra-processed food consumption and obesity among the Australian adult population and stratifying by age group, sex and physical activity level. Methods A cross-sectional analysis of anthropometric and dietary data from 7411 Australians aged ≥20 years from the National Nutrition and Physical Activity Survey 2011–2012 was performed. Food consumption was evaluated through 24-h recall. The NOVA system was used to identify ultra-processed foods, i.e. industrial formulations manufactured from substances derived from foods and typically added of flavours, colours and other cosmetic additives, such as soft drinks, confectionery, sweet or savoury packaged snacks, microwaveable frozen meals and fast food dishes. Measured weight, height and waist circumference (WC) data were used to calculate the body mass index (BMI) and diagnosis of obesity and abdominal obesity. Regression models were used to evaluate the association of dietary share of ultra-processed foods (quintiles) and obesity indicators, adjusting for socio-demographic variables, physical activity and smoking. Results Significant (P-trend ≤ 0.001) direct dose–response associations between the dietary share of ultra-processed foods and indicators of obesity were found after adjustment. In the multivariable regression analysis, those in the highest quintile of ultra-processed food consumption had significantly higher BMI (0.97 kg/m²; 95% CI 0.42, 1.51) and WC (1.92 cm; 95% CI 0.57, 3.27) and higher odds of having obesity (OR = 1.61; 95% CI 1.27, 2.04) and abdominal obesity (OR = 1.38; 95% CI 1.10, 1.72) compared with those in the lowest quintile of consumption. Subgroup analyses showed that the trend towards positive associations for all obesity indicators remained in all age groups, sex and physical activity level. Conclusion The findings add to the growing evidence that ultra-processed food consumption is associated with obesity and support the potential role of ultra-processed foods in contributing to obesity in Australia.