My fiance says she read a fantasy book in seventh grade, but can't remember the author or much of the story line. She says the book cover was of a tree trunk in slight shadow and also a boy with skin like tree bark. She was in seventh grade in 1999, so I know the book is older than that. The book might also be more on the dark side of fantasy.
The Frightened Forest, by Ann Turnbull
I have not read it myself, but I understand that it is young adult fiction, and that one of the plot elements involves a boy being turned into a tree by an evil witch.
This seems to be the most common cover: