It noted concern, however, with an Iranian military site where nuclear weapons work may have occurred more than a decade ago.
The UN agency said Iran's current level of uranium enrichment, nuclear research and development and other activity is in line with its declarations.
The 21-page report covers Iran's nuclear programme in the run-up to the landmark accord on July 14 and its first steps toward implementing that agreement. A copy of the document was obtained by The Associated Press.
But it offered reservations about the military base of Parchin. Western intelligence agencies say Iran used the site for explosives tests and other experiments related to the development of nuclear weapons.
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Iran argues the evidence is fraudulent; the IAEA is supposed to clear up the allegations by mid-December.
The IAEA said it recently observed through satellite imagery the presence of vehicles, equipment and probable construction materials at the site.
And it warned, "The activities that have taken place at this location since February 2012 are likely to have undermined the agency's ability to conduct effective verification."
It allows Tehran to take its own environmental samples from the site and provide videos and photos to the agency, "taking into account military concerns." IAEA Director General Yukiya Amano has said the arrangements are "technically sound" and consistent with long-established practices.
The UN probe runs parallel to the much bigger nuclear pact Iran reached with the US, Britain, China, France, Germany and Russia. That deal will potentially provide Iran hundreds of billions of dollars in relief from international sanctions in exchange for 15 years of strict controls on its nuclear programme.