Starbucks has said it is "deeply saddened by the senseless acts" in Jakarta.
The company said one customer was injured and treated at the scene, with all employees confirmed safe.
"Our hearts are with the people of Indonesia," the company said in a statement.
"Amidst reports of attacks targeting police posts throughout central Jakarta, initial reports are that an explosion took place close to our store in the Skyline building near one of these police posts.
"This store and all other Starbucks stores in Jakarta will remain closed, out of an abundance of caution, until further notice."
Twitter members in Indonesia have begun using the hashtag #KamiTidakTakut, meaning "We Are Not Afraid", following the deadly attacks in the capital.
Several people have been killed in a series of co-ordinated bomb and gun attacks in Jakarta.
Four suspected militants have been killed and the area is being secured after a siege in the Indonesian capital Jakarta, a police spokesman said.
A police spokesman said officers were "sterilising the building" after a gunbattle between the attacks and police took place in a cinema.
"We will declare the situation secure soon," he said.
There is no indication at present that so-called Islamic State is responsible for the attack on the Indonesian capital Jakarta, the head of the national intelligence agency has said.
"This is definitely terrorism but there are no indications yet that it's ISIS related," said Sutiyoso.
Indonesian president Joko Widodo has said the situation in the country's capital is under control following a series of bomb and gun attacks.
"The state, nation and people should not be afraid of, and lose to, such terror acts," he said.
He condemned the attacks, adding: "We express condolence to those who became victims, but we all also condemn the attack that caused restless among the community."
Mr Jokowi has cut short a planned engagement to return to Jakarta.
At least one fresh explosion has been heard in the Indonesian capital, as police hold an armed stand-off with militants that attacked the city centre.
Al Jazeera reported that several gunmen are thought to be hiding in a cinema near the affected area, with a reporter at the scene saying "a lot of people are believed to be inside".
"Police has the building surrounded. The situation there is very unclear," he said.
At least six people have been killed after militants launched a gun and bomb assault in the centre of the Indonesian capital Jakarta, police said.
One explosion took place in a Starbucks cafe, where security forces were later seen entering.
A police spokesman said it was not yet known who was responsible but added they had previously had a threat from so-called Islamic State that "Indonesia will be in the spotlight.
Local station Metro TV reported that up to 14 gunmen were involved in the attack.
Three police officers and three civilians had been confirmed dead so far, he said.
Gunfire is still being reported in the city, though police denied reports of hostages being taken.
At least three people have died after explosions and gunfire were reported in Jakarta, Indonesia.
One of the blasts was reported to have taken place in a Starbucks cafe, after which a Reuters photographer said he saw the bodies of three people.
Several explosions have been heard in the Indonesian capital of Jakarta, with reports of casualties seen.
Witnesses told the Reuters news agency the blasts had been heard in the centre of the capital, while a UN regional representative tweeted to say six bombs had gone off, followed by a "serious exchange of gunfire".
And now a serious exchange of fire in the street
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