Since taking office in February, Health Secretary Robert F. Kennedy Jr. has put an unmistakable stamp on American vaccine policy.

He has effectively restricted access to Covid shots, installed skeptics to influential posts and ousted the director of the Centers for Disease Control and Prevention after she defied his orders on inoculations.

But Mr. Kennedy has applied a far lighter touch to what he and his Make America Healthy Again movement have described as the other major scourge plaguing American children: pesticides and unhealthy foods.

Far from cracking down on food and farming practices, Mr. Kennedy’s MAHA commission report on Tuesday defended existing pesticide review procedures and, in some cases, called for loosening food regulations, even as the report promised future steps to clean up what children eat.

To many scientists — and some of Mr. Kennedy’s own followers — the gap between the health secretary’s use of his authority over food quality and his pummeling of vaccines has created a jarring split screen.

“It seems like the vaccine issues were very much like, ‘Go ahead, Bobby, here’s your green light, do what you want,’” said Elizabeth Frost, a MAHA organizer in Ohio. “It feels like it’s a very different conversation and a very different environment around pesticides and food.”