Extra security precautions were taken ahead of Obama's arrival following terrorist attacks in France, Egypt and Lebanon.
At least 2,000 army personnel were being stationed at strategic points in Kuala Lumpur and another 2,500 were on standby, Armed Forces chief Zulkifeli Mohd Zin said.
Here are some of the highlights of his second visit to the capital.
Earlier on Friday, before Obama's arrival, a Solidariti Anak Muda Malaysia (SAMM) held a protest outside the US embassy here, to protest against the Trans-Pacific Partnership Agreement (TPPA).
The world leader who is also referred to as POTUS (President of The United States) on social media attended his first event after arriving, at the town hall session of Young Southeast Asian Leaders Initative (YSEALI) at Taylor's University, Petaling Jaya.
The session proved to be a good platform for local and international youths to interact and voiced their concerns towards some issues in their respective countries.
PHOTO GALLERY: Barack Obama during town hall meeting with alumni of the YSEALI
YSEALI connected leaders from across the region and offered an array of resources, online networking opportunities and professional training.
After what seemed to be an inspiring talk with the university students, Obama headed for a bilateral talk with Prime Minister Datuk Seri Najib Tun Razak at the Kuala Lumpur Convention Centre (KLCC).
Najib at a joint-press conference after the meeting said Malaysia and the United States have agreed to make Malaysia a counter-messaging centre to fight extremism.
Najib said the counter-messaging centre initiative was important because in fighting extremism "not only a military solution is required but winning the hearts and mind of the people".
On his second day of the trip, Obama spoke about TPPA in his speech at the ASEAN Business and Investment Summit 2015.
Stressing that TPPA) is not just a trade pact, Obama said it is also a future which is secure and upholds the universal right of every human being.
The US president also spoke about the Mali bombing, condemning what he called the "appalling" attack in Mali that left at least 27 people dead, including an American citizen.
"This barbarity only stiffens our resolve to meet this challenge," he said.
Later, Obama had also taken time to visit the Dignity For Children Foundation in Sentul, a charity-based educational institution for refugee and urban poor children.
Ditching protocol, the father of two stopped to talk to the children, interacting with some of them from Myanmar who seemed unperturbed with his presence at the centre. The children continued working on their art and science projects, asking them about their favourite subjects and ambitions as he offered words of encouragement.
Following the visit to the centre, Obama met a group of social activists in an hour-long meeting to discuss issues on TPPA, corruption and human rights, as well as corruption allegations involving national strategic investment fund, 1Malaysia Development Berhad (1MDB).
Among those present at the meeting were National Human Rights Society president Datuk Ambiga Sreenevasan; Bersih 2.0 chairman Maria Chin Abdullah; and Centre to Combat Corruption and Cronyism executive director, Cynthia Gabriel.
Obama also held a press conference at Ritz Carlton, KL attended by journalists and crew members from local and international media.
At the press conference, he urged global communities and world leaders to not succumb to fear if they wish to combat terrorism.
At the same time, he also refused to comment about any allegations concerning Prime Minister Najib, saying that he will not comment on investigations being done in a foreign country.
The US President left Malaysia from TUDM, Subang at 5.45 pm.
