The world leader will be joining leaders of the 10-member Association of South East Asian Nations (ASEAN) for a weekend summit.
Leaders from eight other countries with close partnerships with the grouping - Australia, China, India, Japan, New Zealand, Russia, South Korea and the United States - will also attend the meetings starting on Saturday.
Obama in his visit this time is expected to raise three important issues; Opposition and human rights issue in Malaysia, the Trans-Pacific Partnership Agreement (TPPA) and the South China Sea which China is laying claim.
1. Status of the opposition and respect for human rights
The Opposition leader was jailed in February following the Court’s decision over the charges that he had sodomised his former aide Saiful Azlan Bukhari.
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US Deputy National Security Adviser Ben Rhodes told reporters at an Asia-Pacific summit in Manila that Obama will "very directly" raise concerns about the status of the opposition and respect for human rights when he visits Malaysia.
"We are going to be very candid about areas where we have disagreements and differences and frankly objections, if we see that the type of universal values that we support are not being respected," Rhodes said.
"The president ... will raise with Prime Minister Najib concerns we have about the status of the political opposition in Malaysia, the imprisonment of elements of that opposition or of free media and civil society that are such important components of democracy," Rhodes said.
Obama is also expected to meet representatives of Malaysia's civil society and youth organisations.
2. Trans-Pacific Partnership Agreement
Deputy Foreign Minister Datuk Seri Reezal Merican Naina Merican had earlier this month denied claims that the visit by Obama here is to put pressure on Malaysia to sign the TTPPA.
He also said Obama's visit here was not intended to put pressure on any agreement for the purchase of aircraft or arms.
The US is the key proponent of the TPPA and has been pushing for Malaysia to sign the deal.
International Trade and Industry Minister Datuk Seri Mustapa Mohamed had last month said TPPA is vital in ensuring that Malaysia remains competitive.
He also guaranteed that domestic sentiment will always be protected.
Mustapa said, Malaysia can withdraw anytime from TPPA even upon implementation, if "uncomfortable" with it and added that it will not be penalised for doing so as the TPPA was a voluntary agreement.
3. South China Sea
China’s maritime assertiveness in the South China Sea has caused alarm among its neighbours in particular Malaysia, Brunei, Vietnam and the Philippines.
The four ASEAN countries claim parts of the South China Sea, a key shipping lane believed to be rich in undersea gas deposits.
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But China says almost all of the sea is its own, including waters near to the shores of its smaller neighbours.
Subi Reef, which lies close to the Philippines in the South China Sea, used to be submerged at high tide before China began a massive dredging project to turn it into an island. It is now big enough to potentially host an airstrip.
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China has built small islands on top of previously submerged reefs like Subi and is in the process of smoothing and reinforcing runways suitable for military aircraft. According to international law, experts said no country can claim more than a 500-meter safety zone around a previously submerged reef.
