Previous investigations on protein associations with diet quality and obesity still have inconclusive findings, possibly due to how protein intake was expressed. This study aimed to compare how different ways of expressing total protein intake may influence its relationships with diet quality and obesity. Usual protein intake was estimated from the 2011–12 Australian National Nutrition and Physical Activity Survey (n = 7637 adults, ≥19 years), expressed in grams (g/d), percent energy (%EI), and grams per actual kilogram body weight (g/kgBW/d). Diet quality was assessed using the 2013 Dietary Guidelines Index, and obesity measures included Body Mass Index (BMI) and waist circumference (WC). Sex-stratified multiple linear and logistic regressions were performed and adjusted for potential confounders. Total protein (g/d) was directly associated with diet quality (males, β = 0.15 (95% CI 0.12, 0.19); females, β = 0.25 (0.22, 0.29)), and this association was consistent across units. Protein intake (g/d) was directly associated with BMI (males, β = 0.07% (0.04%, 0.11%); females, β = 0.09% (0.04%, 0.15%)), and WC (males, β = 0.04 (0.01, 0.06); females, β = 0.05 (0.00, 0.09)). While in males, protein as %EI was associated with higher WC, no association was found in females. Adults with higher protein intake (g/d) had higher odds of overweight/obesity (males, OR = 1.01 (1.00, 1.01); females, OR = 1.01 (1.00, 1.01)), and central overweight/obesity (females, OR = 1.01 (1.00, 1.01)), but no significant association with females odds of overweight/obesity when protein was expressed in %EI. In conclusion, protein intake was positively associated with diet quality and obesity, yet these associations were stronger for women. The effect sizes also varied by measurement unit due to the different scales of those units.