Iran's reported stockpile of low-enriched uranium had increased to 1,508 kg, almost 200 more than in May.
Nuclear analysts said the production rate, around 50 percent capacity, appeared the same, albeit with fewer centrifuges on stream.
The report said Iran had assented to improved IAEA camera surveillance and data collection in the underground Natanz enrichment hall, and a plan for unannounced inspections.
"This satisfies our requirements for a bigger facility," a senior UN official, speaking on condition of anonymity.
The deal came after the IAEA complained that Iran's headlong expansion of centrifuge operations since 2008, without allowing corresponding monitoring upgrades to keep pace, had left non-proliferation inspectors unable to verify that no equipment or materials were being diverted for weapons purposes.
Friday's report distilled the IAEA's struggle to verify whether Iran indeed has illicitly combined uranium processing, airborne high-explosive tests and work to remodel a missile cone with the apparent purpose of devising a nuclear payload.
While the IAEA cited no proof of an outright bomb project, it said the intelligence was compelling and Iran must do more to resolve suspicions than merely brand it as a fabrication.
"The information ... appears to have been derived from multiple sources over different periods of time, appears to be generally consistent, and is sufficiently comprehensive and detailed that it needs to be addressed by Iran with a view to removing the doubts which naturally arise, in light of all of the outstanding issues, about the exclusively peaceful nature of Iran's nuclear programme," the report said.
Iran had acknowledged some activities outlined in the intelligence and denied they had nuclear use but was withholding documentation, refusing access to locations and officials for interviews needed by the IAEA to check its assertions, it said.
The IAEA said Iran also allowed inspectors to revisit the Arak heavy-water reactor site this month after barring access for a year.
The West suspects Iran is pursuing the means to produce atomic bombs under cover of a civilian nuclear fuel programme.
Iran says it wants only electricity from nuclear power and has again rejected UN demands for a halt.