Steve Jobs’ resignation as Apple CEO will spawn some soul-searching on Infinite Loop in the days and weeks ahead, as Apple’s 49,000 employees decide exactly where their loyalties lie, according to researchers who study the effects of leadership change on organizations.

“Employees are asking themselves, ‘Was I working for Apple or for Steve?’ If the answer is Steve, they will wonder if Apple will be the same place without him,” said Gary Ballinger of the University of Virginia, who studies how departing bosses affect employees and other components of a company.

Though Jobs’ departure from Apple...