VIENNA—Iran carried out its threat to enrich uranium at its underground Fordow nuclear site, the United Nations atomic agency said Monday, confirming Tehran’s most serious step yet away from the 2015 nuclear deal.

Iran has taken a series of steps since July to step away from the nuclear deal, a set of calibrated responses to harsh U.S. sanctions designed to pressure Europe into helping Tehran economically and persuade the White House that its maximum-pressure sanctions policy is leading Iran back to the brink of being a breakout...