While the next 180 days will be rough for Rousseff -- she will have to face up to accusations that she broke budget laws -- Temer has the immensely difficult task of winning back the trust of Brazilians.
Aside from juggling the precarious state of the Brazilian economy, Temer must deal with a Zika virus epidemic and a fraught 2016 Olympics.
"It is urgent to calm down the nation and unify all of us," Temer said in a televised address shortly after assuming office.
"Brazil lives today in the worst economic crisis of our history -- 11 million unemployed, inflation up two digits, deficit of 100 billion reals and the situation of health care in Brazil is chaotic," he said.
"Our challenge is to restore this free fall of the economy which has increased unemployment and loss of lifestyle of population," he said. "So it is imperative that we rebuild the fundamentals of Brazilian economy and improve the environment for businesses so that they can do what they are supposed to be doing: produce, invest and create jobs."
On day one, Temer immediately implemented several new changes in the government. But not all of them went down well.
He unveiled a Cabinet that trimmed the number of ministers from 31 to 22 in a concerted effort to cut costs, but was entirely made up of white men.
It's the first time since 1979, when the country was controlled by a military dictatorship, that there hasn't been a single woman in the Cabinet.
Back in April, Rousseff blamed sexism
for the push to oust her, saying her gender was a "strong component" of her impeachment.
The internet was quick to point out the lack of diversity in the Cabinet.
"First government without women since Geisel. Not even the end of the dictatorship dared to be so sexist," one tweeted.
"No women or blacks in Temer's government. An 100% big patriarchal house. The bridge to the past has opened and we advance towards it," said another.
Meanwhile, his appointment of soybean tycoon Blairo Maggi, who stepped into the position of agriculture minister, set off alarm bells with environmentalists.
"Blairo Maggi in the Ministry of Agriculture? Isn't he the biggest soya farmer in the country? I'm confused!"
"The King of Soya' in the Ministry of Agriculture. I never thought I would ever find Katia Abreu reasonable ... Bye bye, Amazon Forest!"
Temer appointed a new sports minister too -- Leonardo Picciani -- just 85 days before the Rio 2016 Olympics opening. Picciani is the third person to fill the post in as many months.
He'll be working with Ricardo Barros, the new health minister, to ensure the games go smoothly.
More than 10,000 athletes and 500,000 visitors are expected to gather in the city when the games kick off on August 5. But experts have accused Brazil of being irresponsible for not postponing or relocating the games while Zika poses a health threat.
Amir Attaran of the University of Toronto says not delaying or moving the games would run the risk of spreading the virus globally.
"The question is really -- and it's an ethical one -- is it worth having the games in Rio when you could have it elsewhere or just delay your pleasure a little bit so as not to run the horrible risk of outbreak of -- I hate to say it -- shrunken brain babies?" Attaran said.
The World Health Organization issued several health recommendations Thursday on the Rio Olympics
, including that visitors should use insect repellant and avoid over-crowded and poorly-sanitized areas.
Meanwhile, Brazil soccer legend Rivaldo has said the country is getting "more ugly" and has warned visitors to "stay away
," citing the violence in the city.
But the International Olympic Committee said Thursday that it remains confident the Summer Olympics will be a success.
"There is strong support for the Olympic Games in Brazil and we look forward to working with the new government to deliver successful Games in Rio this summer," officials said.