He has moved quickly after a campaign in which the far-right leader said he would radically overhaul many aspects of life in Latin America’s largest nation.
Meanwhile, Sao Paulo’s stock market jumped 3.56 per cent to a record closing of 91,012 points as new cabinet ministers reinforced the intent to privatise state-owned companies and a Brazilian arms maker benefited from Mr Bolsonaro’s plans to loosen gun controls.
Similar spikes in stock prices also occurred during the presidential campaign.
One of the orders issued late on Tuesday, hours after Mr Bolsonaro’s inauguration, is likely to make it all but impossible for new lands to be identified and demarcated for indigenous communities.
Areas set aside for “Quilombolas”, as descendants of former slaves are known, are also affected by the decision.
Another order removed the concerns of the LGBT community from consideration by the new human rights ministry.
In a move favourable to his allies in agribusiness, which have criticised giving large swaths of lands to the indigenous, Mr Bolsonaro transferred the responsibilities for delineating indigenous territories from the Justice Ministry to the Agriculture Ministry.
The new agriculture minister, Tereza Cristina, is part of the agribusiness caucus in Brazil’s lower house and has opposed requests from native communities.
Mr Bolsonaro, a former army captain and longtime congressman, said during his presidential campaign that he would stop making what he calls concessions to native Brazilians and Quilombolas.
“Less than one million people live in those places isolated from the real Brazil,” he tweeted on Wednesday.
“They are explored and manipulated by non-profits. Together we will integrate those citizens and give value to all Brazilians.”
The Justice Ministry previously handled demarcation of indigenous lands through the FUNAI agency, which also oversees other initiatives for indigenous groups such as health care, housing and language preservation.
Mr Bolsonaro’s order is raising uncertainties about FUNAI by shifting it to a new ministry for family, women and human rights that is headed by an ultraconservative evangelical pastor.
Observatorio do Clima, a network of 45 Brazilian civil society groups, criticised the executive orders, calling them “only the first step on meeting Mr Bolsonaro’s campaign promises of dismantling environmental governance, stripping indigenous peoples of their rights and opening up indigenous lands for business”.
“The attack on FUNAI goes beyond the wildest dreams of the rural caucus, who had tried for years to pass a constitutional amendment transferring the demarcation of indigenous lands from the president to Congress,” the nonprofit said.
“Bolsonaro solved the problem by transferring them directly to farmers.”
The far-right leader said last year that he also wants to annul land demarcation decisions made by previous administrations, but legal experts say recent Brazilian Supreme Court rulings could block such move.
New health minister Luiz Henrique Mandetta also suggested on Wednesday that there will be spending cuts in health care for the indigenous.
“We have figures for the general public that are much below what is spent on health care for the indigenous,” he said, without providing details.
In removing LGBT concerns from the responsibilities of the human rights ministry, Mr Bolsonaro did not name any agency to consider such issues.
He has strongly criticised what he calls “gender-based ideology”, saying it is a threat to Brazil’s Christian values.
Damares Alves, the new human rights minister, did not discuss the LGBT order in her first address on the job, but the evangelical pastor has insisted over the years that “the Brazilian family is being threatened” by diversity policies.
On Wednesday, she said: “The state is lay, but this minister is terribly Christian.”
Under the new administration, "girls will be princesses and boys will be princes. There will be no more ideological indoctrination of children and teenagers in Brazil”, Ms Alves added.
LGBT activist Symmy Larrat said she does not expect reasonable treatment from the Bolsonaro administration.
“The human rights ministry discussed our concerns at a body called secretariat of promotion and defence of human rights.
"That body just disappeared, just like that. We don’t see any signs there will be any other government infrastructure to handle LGBT issues,” she said.
The newspaper Folha de S.Paulo reported that Bolsonaro will later announce the closing of an agency within the Education Ministry that has been aimed at promoting diversity in public schools and universities.
New foreign minister Ernesto Araujo indirectly criticised the LGBT community as being “those that say they are not men and women”.
Also on Wednesday, the Brazilian Press Association criticised restrictions on journalists at Mr Bolsonaro’s inauguration.
Reporters had to arrive seven hours before the events began and were forbidden to move freely in Congress and the presidential palace. Food was seized and access to bathrooms and water was limited.
“What was seen in different scenarios of Brasilia is incompatible with a democratic regime,” the association said in a statement.
"Respect to the press is one of the main indicators of nations that consider themselves civilised.”
Mr Bolsonaro’s first day in office sparked a wave of optimism in Brazil’s financial market. Stocks of Brazil’s electric-company Eletrobras soared more than 20 per cent.
Arms maker Taurus, one of the main allies of the new president, jumped more than 47 per cent.
Mr Pompeo told him that Mr Trump is “very pleased with the relationship that our two countries are on the precipice of beginning to develop”.
“He’s also confident that [the relationship between the US and Brazil] will benefit the world and the set of shared values that we believe we can together advance,” Mr Pompeo said before leaving Brazil for Colombia.
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