A method of providing a whole-grain flour having reduced lipase enzyme activity using a multi-stage deactivation process in a grain processing system, the system comprising: a hydration chamber arranged and configured to provide steam hydration; a microwave chamber after the hydration chamber; a breaking device positioned between the hydration chamber and the microwave chamber; a conveyor connecting the hydration chamber to the microwave chamber; the method comprising: separating a flour fraction having endosperm from a milled bran fraction having bran and germ, the milled bran fraction having a lipase enzyme activity; subjecting the milled bran fraction to a steam treatment step, whereby the bran fraction is exposed to steam having a temperature of 100 to 150°C and a pressure of 16.54kPa to 337.8kPa (2.4 to 49 psi) for 60 to 180 seconds, in the hydration chamber effective to hydrate the milled bran fraction and to deactivate a first portion of the lipase enzyme activity to provide a hydrated bran fraction; conveying the hydrated bran fraction to the breaking device to break apart any agglomerates of the hydrated bran fraction that form in the hydration chamber; subjecting the hydrated bran fraction to a drying treatment step using microwave energy at 5 kW to 100 kW at 915 MHz to 20 GHz for 60 to 180 seconds in the microwave chamber effective to dry the hydrated bran fraction and to deactivate a second portion of the lipase enzyme activity to provide a treated bran fraction, whereby the lipase enzyme activity in the treated bran fraction is reduced relative to the milled bran fraction by 77 to 100 percent; and combining the treated bran fraction with the separated flour fraction to provide a whole-grain flour having reduced lipase enzyme activity; and wherein a total time of the combined steam and drying treatment steps is less than 600 seconds. a hydration chamber arranged and configured to provide steam hydration; a microwave chamber after the hydration chamber; a breaking device positioned between the hydration chamber and the microwave chamber; a conveyor connecting the hydration chamber to the microwave chamber; the method comprising: separating a flour fraction having endosperm from a milled bran fraction having bran and germ, the milled bran fraction having a lipase enzyme activity; subjecting the milled bran fraction to a steam treatment step, whereby the bran fraction is exposed to steam having a temperature of 100 to 150°C and a pressure of 16.54kPa to 337.8kPa (2.4 to 49 psi) for 60 to 180 seconds, in the hydration chamber effective to hydrate the milled bran fraction and to deactivate a first portion of the lipase enzyme activity to provide a hydrated bran fraction; conveying the hydrated bran fraction to the breaking device to break apart any agglomerates of the hydrated bran fraction that form in the hydration chamber; subjecting the hydrated bran fraction to a drying treatment step using microwave energy at 5 kW to 100 kW at 915 MHz to 20 GHz for 60 to 180 seconds in the microwave chamber effective to dry the hydrated bran fraction and to deactivate a second portion of the lipase enzyme activity to provide a treated bran fraction, whereby the lipase enzyme activity in the treated bran fraction is reduced relative to the milled bran fraction by 77 to 100 percent; and combining the treated bran fraction with the separated flour fraction to provide a whole-grain flour having reduced lipase enzyme activity; and separating a flour fraction having endosperm from a milled bran fraction having bran and germ, the milled bran fraction having a lipase enzyme activity; subjecting the milled bran fraction to a steam treatment step, whereby the bran fraction is exposed to steam having a temperature of 100 to 150°C and a pressure of 16.54kPa to 337.8kPa (2.4 to 49 psi) for 60 to 180 seconds, in the hydration chamber effective to hydrate the milled bran fraction and to deactivate a first portion of the lipase enzyme activity to provide a hydrated bran fraction; conveying the hydrated bran fraction to the breaking device to break apart any agglomerates of the hydrated bran fraction that form in the hydration chamber; subjecting the hydrated bran fraction to a drying treatment step using microwave energy at 5 kW to 100 kW at 915 MHz to 20 GHz for 60 to 180 seconds in the microwave chamber effective to dry the hydrated bran fraction and to deactivate a second portion of the lipase enzyme activity to provide a treated bran fraction, whereby the lipase enzyme activity in the treated bran fraction is reduced relative to the milled bran fraction by 77 to 100 percent; and combining the treated bran fraction with the separated flour fraction to provide a whole-grain flour having reduced lipase enzyme activity; and wherein a total time of the combined steam and drying treatment steps is less than 600 seconds.