The effect of thermal processing via autoclaving on modifications of total phenolics, antioxidant activity and functionality of wheat, buckwheat, corn and oats sprouts and seedlings were investigated. Functionality for type 2 diabetes related α-amylase, α-glucosidase inhibition and levo-dihydroxy phenylalanine ( l-DOPA) content, hypertension related angiotensin converting enzyme 1 (ACE) inhibition and ulcer related Helicobacter pylori inhibition were evaluated using in vitro assays. Thermal processing in general resulted in tissue browning leading to higher total phenolic content and free radical scavenging-linked antioxidant activity. It increased α-amylase inhibitory activity in buckwheat and oats but decreased in wheat and corn sprouts and seedlings. It increased α-glucosidase inhibitory activity in wheat, buckwheat and oats but decreased in corn sprouts. It reduced the cognitive function/diabetes related l-DOPA content in all grains sprouts and seedlings tested. It increased ACE inhibitory activity in buckwheat and oats, but decreased in wheat and corn sprouts. It also improved the ulcer related H. pylori inhibitory activity in all grain sprouts and seedlings studied. These changes in functionality are suggested to be due to modifications in the total phenolic content and profile by phenolic oxidation or polymerization caused by thermal processing. Therefore, diet designs for chronic disease management will have to consider thermal processing-linked modification of bioactive ingredient profiles. Thermal processing altered the total phenolic content and antioxidant activity in winter wheat, buckwheat, corn and oats sprouts and seedlings. It modified the α-amylase inhibitory activity, α-glucosidase inhibitory activity, l-DOPA content, ACE inhibitory activity and H. pylori inhibitory activity of samples. Therefore, the food processing industry and diet design for chronic disease management will have to consider thermal processing-linked modification of bioactive ingredient profiles for more effective health benefits.