Obama will land in Manila hours after the allies sign a new defence agreement allowing rotations of US troops and ships through the Philippines, part of a US rebalancing of military power towards rising Asia.
Anti-China sentiments run high in the Philippines, which is locked in a showdown with the Asian giant over disputed atolls in the South China Sea, part of a proliferation of maritime hotspots that has stoked Asian tensions.
During an Asian tour that has taken him to Japan, South Korea and Malaysia, Obama has repeatedly warned that small nations should not be bullied by larger ones, a clear reference to China's increasingly sharp geopolitical elbows.
"Disputes need to be resolved peacefully, without intimidation or coercion, and... all nations must abide by international rules and international norms," Obama said in Malaysia Sunday.
That is also a message that has resonance in America's East-West showdown with Russia over Ukraine -- a row to which Obama has had to return time an again during his Asian journey.
- Simmering disputes -
Opening his trip Obama made clear that US defence treaties with Japan did cover disputed islands long administered by Tokyo in the East China Sea, which are known as the Senkakus in Japan and Diaoyus in China.
The Philippines has its own territorial disputes with China in the South China Sea -- notably over the Second Thomas Shoal, an outpost in the remote Spratly Islands.
US officials have not been so specific over perceptions of their obligations towards Manila on territorial disputes -- but it is clear they do not believe them covered by the American Mutual Defense Treaty with the Philippines.
"With respect to some of the difficult territorial issues that are being worked through, it is hard to speculate on those because they involve hypothetical situations in the South China Sea," said deputy national security advisor Ben Rhodes.
"The US Japan agreement has very specific coverage of territory under Japanese administration.
"Some of the disputes in the South China Sea raise more hypothetical circumstances."
In essence, the difference lies in the fact that Japan already administers the Senkakus/Diaoyus while the status of other islands and reefs is disputed -- even though they lie within the Philippines' internationally-mandated exclusive economic zone and more than 1,000 kilometres (580 miles) from the nearest Chinese landmass.
Brunei, Malaysia, and Vietnam, as well as Taiwan, also have overlapping claims to the sea, believed to contain vast deposits of natural gas and oil.
Obama has repeatedly stressed that despite Beijing's territorial disputes with its allies, his Asia rebalancing strategy is not aimed at containing China's rise to regional, and perhaps global super power status.
But officials also make clear that they blame China for hiking tensions in the region over claims often well outside its territorial waters.
"We oppose the use of intimidation, coercion or aggression by any state to advance their maritime territorial claims," said Evan Medeiros, senior director for Asia at the National Security Council.
- US 'rebalance' to Asia -
The Philippines has accused China of becoming increasingly aggressive in staking its claims to the sea, and has called on the United States for greater military as well as diplomatic support.
During his overnight stay in the Philippines, his first visit as president and his last stop on this Asian journey, Obama will meet President Benigno Aquino, hold a press conference and attend a state dinner. The new defence agreement will not allow Washington to establish a permanent base in the Philippines or bring in nuclear weapons to the country.
But it represents a new era in defence ties. The Philippines hosted two of the largest overseas US military bases until 1992, when Manila voted to end their lease amid growing anti-US sentiment.
Amid rising regional disquiet over the implications of China's rise, the Philippines has sought greater military ties with Washington in recent years. John Blaxland, a security analyst at the Australian National University said that the new defence deal would be seen as an important US assurance for Manila.
"The presence, and the aura of the presence is something that the Philippines desperately wants, and is something that the US sees as being necessary to effect the rebalance to Asia," said Blaxland.
"Bolstering the US presence will undoubtedly induce the Chinese to think hard about ratcheting further the confrontation with the Philippines in the South China Sea."