Boxes of brightly colored breakfast cereals, vivid orange Doritos and dazzling blue M&Ms may find themselves under attack in the new Trump administration.

In excoriating such grocery store staples and their mysterious ingredients, Robert F. Kennedy tapped into a zeitgeist of widening appeal for healthy foods to curb obesity and disease that helped propel President-elect Donald J. Trump to select him to oversee the country’s vast health agency.

“We are betraying our children by letting these industries poison them,” Mr. Kennedy said at a campaign rally on Nov. 2, to raucous applause.

As Mr. Trump’s choice to head the Department of Health and Human Services, he would have far-reaching authority over the Food and Drug Administration, which regulates about 80 percent of the nation’s food supply. That includes shaping regulations on packaging that declares something “healthy” or discloses the amounts of sugar, salt and other ingredients in most packaged foods.

But in vowing to upend the nation’s food system, Mr. Kennedy is taking a direct shot at Big Food, one of the country’s most powerful industries whose traditional allies are Republicans. Even something as simple as removing artificial dyes is likely to result in a knockdown battle for the multibillion-dollar food sector, which is wary of higher manufacturing costs or a dip in sales of products favored by loyal consumers.

More broadly, Mr. Kennedy has set an agenda to root out what he considers corruption in the arena of government and public health, arguing that regulatory agencies overseeing food and drugs have been working hand in hand with corporate America to enhance profits rather than to benefit consumers.