As Saudi Crown Prince Mohammed bin Salman pushed through ambitious social reforms, he also ordered a zero-tolerance campaign against dissent spearheaded by his most trusted confidant, who is now implicated in the murder of journalist Jamal Khashoggi.

People with knowledge of the work of Saud al-Qahtani say he was intimately involved in the kingdom’s targeting of Mr. Khashoggi—from efforts to persuade him to return to Saudi Arabia from the U.S., to the planning and execution of the operation that ended with his death in the Saudi consulate in Istanbul on Oct. 2. He is under criminal investigation, these people say, and has been fired from his job as the crown prince’s media adviser.

The alleged role of Mr. Qahtani in the murder is complicating Saudi Arabia’s efforts to separate its de facto leader, Prince Mohammed, from a killing that has triggered a diplomatic crisis for the kingdom and caused deep angst among the country’s rulers.

“Whether or not he knew about it,” a Western official said of the crown prince, “this happened under his watch.”

Mr. Qahtani and Saudi government representatives didn’t respond to requests for comment.