Tropical storm Hagupit is heading to Manila, but has been downgraded from a typhoon after crossing the country.
At least 27 people were killed by the storm, the Red Cross said, with the eastern island of Samar worst hit, but it caused far less damage than feared, the BBC reported.
Thousands of people are heading home after about a million people were evacuated from vulnerable areas.
The city of Tacloban, which bore the brunt of Super Typhoon Haiyan last year, has emerged relatively unscathed.
Albay province, which evacuated more than half its population, has called for those people to go home.
In the capital, residents are preparing for heavy rain and strong winds.
The typhoon is still travelling westwards across the Philippines, and has weakened into a tropical storm, according to the Philippine meteorological authorities.
A government alert on Monday morning stated that residents of the capital and surrounding regions should expect winds of up to 100km/h in the next 24 hours and to prepare for possible flash floods, landslides, and storm surges of up to 2 metres.
Thousands who live along the coast and riverbanks were evacuated on Monday, reports said. A total of 11.8 million people live in the national capital region.
Manila Mayor Joseph Estrada said the city was "prepared and trained for this", but added: "It's the flooding that we are worried about."
Financial markets closed their doors on Monday along with schools and government offices. Flights and other public transport were halted.
Hagupit has been nowhere near as powerful as Typhoon Haiyan - known as Yolanda in the Philippines - which tore through the central Philippines in November 2013, leaving more than 7,000 dead or missing.
In Tacloban, Hagupit blew away roofs and flooded streets, but the area has escaped the wider devastation of last year.
A total of 183 flights had been cancelled and five airports closed, the agency said, and there were power outages in 16 provinces.