Tropical storm Hagupit is heading to Manila, but has been downgraded from a typhoon after crossing the country.
At least 21 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.
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.
At the scene: Saira Asher, BBC News, Albay province
Albay province, which evacuated more than half its population, has called for those people to go home.
After spending three days at a school in Polangi, families are packing into small military trucks, holding one or two plastic bags with the essentials they brought with them.
They worry about the state in which they'll find their homes but many are most worried about their rice fields, their only source of income.
One woman reached her house and found it flooded and uninhabitable. For her that means at least one more night in the evacuation centre.
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 (62mph) in the next 24 hours, and to prepare for possible flash floods, landslides, and storm surges of up to 2m.
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.
"There were no bodies scattered on the road, no big mounds of debris," local woman Rhea Estuna told the Associated Press by phone from Tacloban. "Thanks to God this typhoon wasn't as violent."
Tacloban Mayor Alfred Romualdez told the BBC that the immediate task was assessing damage to the temporary shelters in which some people have been living.
He said that the weather was good now but that high tides were making it harder for waterways to drain, despite work to clear debris.
UN official Orla Fagan told Reuters that a lot of people have begun returning to their homes. "In Tacloban this morning, the sun is shining, people just started going back," she said.
The storm made its fourth landfall on Monday night, hitting Batangas province some 100km (60 miles) south of Manila with winds of roughly 100km/h.
At its height, as it approached land on Saturday, gusts of up to 250km/h were recorded.
The authorities said they were better prepared than when Haiyan struck, and organised the largest peacetime evacuation in the history of the Philippines.
Justin Morgan, Oxfam country director for the Philippines, told the BBC that a key factor was a greater focus on the dangers of storm surges, meaning people were moved away from coastal areas.
Joey Salceda, governor of Albay province, told the BBC no casualties and only "negligible damage" had been reported in his province.
He said the storm had been identified as a threat in late November, giving officials time to identify population at risk, evacuate them two days ahead of the storm and prepare food supplies.
Known locally as Typhoon Ruby, Hagupit has nonetheless caused major damage in several towns in the east.
The Philippine Red Cross said at least 21 people had died over the weekend, with 18 of those on the eastern island of Samar, where Hagupit made landfall on Saturday.
The mayor of Dolores, a town on Samar, said that 80% of homes there had been destroyed. One resident reportedly died after a tree fell on him.
Two more people - a one-year-old girl and a 65-year-old man - died from hypothermia in the central province of Iloilo, the National Disaster Risk Reduction and Management Council said.
A total of 183 flights had been cancelled and five airports closed, the agency said, and there were power outages in 16 provinces.