Ah, and a better match is "Calling All Creeps!", which was adapted to an episode on the Goosebumps TV show.
Ricky Beamer is tortured and harassed by his schoolmates and called names. He has four enemies who are eighth-graders named Wart, Brenda, David and Jared. He is on the school newspaper, which is called Harding Herald. The head of the school newspaper is a bossy eighth-grader named Tasha McClain. She treats sixth-graders like slaves. Ricky's only friend is a girl, named Iris Candler, who is new. A few days before the school newspaper got published, Ricky was in the newspaper room. He was about to get a Pepsi can from the refreshments desk, when two of his enemies, David and Wart, come along. Wart blocks Ricky's way and David says he wants the can of Pepsi. Ricky says he wants it and both of them start snatching it from each other. The can slips from David's grasp and falls on Tasha's keyboard. She calls Ricky a creep and says he is off the paper.
At first, Ricky takes it all as a joke. Then they transform into purple lizard-like creatures with long tongues. They think Ricky is their commander because of what it said in the paper. They say humans are the past and creeps are the future. They ask Ricky where to plant the identity seeds to turn everybody else into creeps. If they do not plant the seeds before they go stale in a week, they will blow their mission and be killed for not completing it.
Just as it looks hopeless for Ricky, Iris arrived and acted as if she was the commander's assistant. Then she gives them a plan to make cookies at the bake sale and sell them for free. They could put the identity seeds in them, because they look like a real chocolate chips. They agree, however, with her plan and go to Iris' house to bake the cookies.
Brenda tells him that when the children eat the cookies, they will transform and all of them will become Ricky's slaves. Since everybody always made fun of him, Ricky decides to give everybody a free cookie. Then at last, he eats one himself. The story ends with Ricky saying that there be changes happening around the school.
I found it by searching for
tv show school lizard people cookies