Ultra-processed foods (UPF), defined using the Nova classification system, are associated with increased chronic disease risk. More recently, evidence suggests the UPF subgroup of whole-grain breads and cereals is in fact linked with reduced chronic disease risk. This study aimed to explore associations of cardiometabolic risk measures with Nova UPF intake v. when foods with ≥ 25 or ≥ 50 % whole grains are excluded from the definition. We considered dietary data from the Australian National Nutrition and Physical Activity Survey 2011–2012. Impacts on associations of UPF intake (quintiles) and cardiometabolic risk measures were analysed using regression models. The median proportion of UPF intake from high whole-grain foods was zero for all quintiles. Participants in the highest Nova UPF intake quintile had significantly higher weight (78·1 kg (0·6)), BMI (27·2 kg/m2 (0·2)), waist circumference (92·7 cm (0·5)) and weight-to-height ratio (0·55 (0·003)) compared with the lowest quintile (P< 0·05). Associations were the same when foods with ≥ 25 and ≥ 50 % whole grains were excluded. Adjusted R-squared values remained similar across all approaches for all outcomes. In Australia, high whole-grain foods considered UPF may not significantly contribute to deleterious cardiometabolic risk associations. Until conclusive evidence on Nova UPF is available, prioritisation should be given to the nutrient density of high whole-grain foods and their potential contribution to improving whole-grain intakes and healthful dietary patterns in Australia.