Many dietary guidelines emphasise “mostly” whole grain food choices as part of an overall healthy eating pattern based on evidence for enhancing nutritional status and reducing chronic disease. Still, countries including Australia fall short of their consumption targets. Furthermore, healthcare cost savings associated with increasing the consumption of whole grains in alignment with the Daily Target Intake (DTI) recommendation of 48 g are unknown. The aim of this study was to assess the potential savings in costs of healthcare and lost productivity associated with a reduction in the incidence of Type 2 Diabetes Mellitus (T2DM) and cardiovascular disease (CVD) through meeting the 48 g DTI recommendation for whole grains among the Australian adult population (>20 years). A three-step cost-of-illness analysis was conducted using input parameters from: 1) estimates of proportions of consumers (5%, 15%, 50%, and 100%) who would increase their current intake of whole grains to meet the recommended DTI in Australia; 2) relative reductions in risk of T2DM and CVD associated with specific whole grain consumption, as reported in meta-analysis studies; and 3) data on costs of healthcare and productivity loss based on monetary figures by national healthcare authorities. A very pessimistic (5% of the population) through to universal (100% of the population) adoption of the recommended DTI was shown to potentially yield AUD 37.5 (95% CI 22.3–49.3) to AUD 750.7 (95% CI 445.7–985.2) million, and AUD 35.9 (95% CI 8.3–60.7) to AUD 717.4 (95% CI 165.5–1214.1) million in savings on annual healthcare and lost productivity costs for T2DM and CVD, respectively. Given such economic benefits of the recommended consumption of whole grains, in exchange for refined grains, there is a real opportunity to facilitate relevant socioeconomic cost-savings for Australia and reductions in disease. These results are suggestive of a much greater opportunity to communicate the need for dietary change at all levels, but particularly through food-based dietary guidelines and front-of-pack labelling initiatives.