President Trump’s last-minute decision to pull back from a retaliatory strike on Iran underscored the absence of appealing options available to him as Tehran races toward its next big challenge to the United States: building up and further enriching its stockpile of nuclear fuel.

Two weeks of flare-ups over the attacks on oil tankers and the downing of an American surveillance drone, administration officials said, have overshadowed a larger, more complex and fast-intensifying showdown over containing Iran’s nuclear program.

In meetings in the White House Situation Room in recent days, Secretary of State Mike Pompeo contended that the potential for Iran to move closer to being able to build a nuclear weapon was the primary threat from Tehran, one participant said, a position echoed by Mr. Trump on Twitter on Friday. Left unsaid was that Iran’s moves to bolster its nuclear fuel program stemmed in substantial part from the president’s decision last year to pull out of the 2015 international accord, while insisting that Tehran abide by the strict limits that agreement imposed on its nuclear activities. Mr. Trump has long asserted that the deal would eventually let Iran restart its nuclear program and did too little to curb its support for terrorism.

[Update: Iranian force exults in downing of U.S. drone with a feast and a prayer]

Now, with the immediate crisis over the drone abating, Mr. Trump has taken several steps to confront the nuclear issue. He has dispatched envoys to the Middle East, in an effort to intensify the sanctions the United States has used to squeeze Iran’s economy, chiefly by choking off its ability to sell oil to the world. The president doubled down on that promise on Saturday, saying that he planned to impose “major” additional sanctions on Monday.