Three alleged members of the Abu Sayyaf terrorist group were arrested on November 10, authorities said, a day before leaders began descending on the capital for the Association of Southeast Asian Nations (ASEAN) summit and other meetings.
"A terror attack could have happened if not for that interdiction," the police said in a statement, adding that pistols and grenades were seized from the suspects.
The high-profile gatherings ended on Tuesday without any security incidents and there was no suggestion world leaders were ever in danger.
The summit meetings were held in sealed off venues to which access was strictly limited.
Police said they monitored one suspect's Facebook posts, in which he hinted at a plan to launch terror attacks in Manila. Police did not say when the suspects were planning to carry out the attacks.
The posts included photos of powerful firearms and improvised explosive devices, with captions saying they would be used to kill "kaffir" (non-Muslims) and "munafiq" (apostates).
However, police added they had asked prosecutors to file charges against the three for having unlicensed handguns, not in relation to a bomb plot.
Philippine police chief Ronald Dela Rosa told reporters officers were checking whether the suspects were linked to previous attacks.
The alleged terrorists included two 19-year-olds and a 24-year-old. They were living in a northern Manila slum, largely populated by Muslim migrants. Police said the men came from the remote island of Basilan, an Abu Sayyaf stronghold around 900 kilometres south of the capital.
Abu Sayyaf originated as a loose network of Islamist terrorists formed in the 1990s with seed money from Osama bin Laden's Al-Qaeda network. It later splintered into factions, with some involved in crimes like kidnapping for ransom.
A faction in Basilan recently pledged allegiance to the ISIS. It besieged the southern city of Marawi in May, sparking a five-month battle with government forces that left over a thousand dead.