Junior officers toppled a junta leader on Friday, saying he had failed to fight jihadist attacks in the country.
On Saturday, several witnesses told AFP they heard gunfire in the centre of the capital Ouagadougou, after which troops once again blocked the main roads in the city, including around the presidency.
Helicopters hovered above the city and shops that had opened for business in the morning shut their doors.
The European Union and the African Union added their voices to a chorus of global condemnation to the change in power.
"The chairperson calls upon the military to immediately and totally refrain from any acts of violence or threats to the civilian population, civil liberties, human rights," the AU said in a statement, calling for the restoration of the constitutional order by July 2024.
AU chief Moussa Faki Mahamat said he was deeply concerned about the resurgence of unconstitutional ousters in the West African nation and elsewhere on the continent.
The European Union warned that the coup put in danger efforts undertaken to restore constitutional order by July 1, 2024 and called for the new authorities to respect previous agreements.
"The European Union also deplores the degradation of the security and humanitarian situation in the country," the bloc's foreign policy chief Josep Borrell said in a statement.
The Economic Community of West African States regional bloc "condemned in the strongest possible terms" the latest seizure of power, calling it "inappropriate."
Burkina Faso's former colonial ruler France told its citizens in Ouagadougou -- believed to number between 4,000 and 5,000 -- to stay home.
The United States called "for a return to calm and restraint by all actors".
On Friday, pre-dawn gunfire erupted in the dusty and spread-out capital around the presidential palace and culminated in the latest coup.
Just before 8:00 pm (2000 GMT) on Friday, more than a dozen soldiers in fatigues appeared on the state television and radio broadcaster to announce the removal of Lieutenant-Colonel Paul-Henri Sandaogo Damiba.
They proclaimed 34-year-old Captain Ibrahim Traore in charge.
"We have decided to take our responsibilities, driven by a single ideal: the restoration of security and integrity of our territory," they said.
"Damiba failed. Since he came to power, the zones that were peaceful were attacked. He took power but then he betrayed us," Habibata Rouamba, a trader and activist said on Saturday.
With much of the Sahel region battling a growing Islamist insurgency, the violence has prompted a series of coups in Mali, Guinea and Chad since 2020.
In January, Damiba installed himself as leader of the country of 16 million after accusing elected president Roch Marc Christian Kabore of failing to beat back the jihadists.
Damiba accused of failure
But with more than 40 percent of the country outside government control, the latest putsch leaders said Damiba, too, had failed.
"Far from liberating the occupied territories, the once-peaceful areas have come under terrorist control," the new military leaders said.
They then suspended the constitution, sealed the borders, dissolved the transitional government and legislative assembly and instituted a 9:00 pm to 5:00 am curfew.
New strongman Traore was previously head of anti-jihadist special forces unit "Cobra" in the northern region of Kaya.
Junta leader's fate unclear
Damiba's fate remains unknown. Though he had promised to make security his priority when he took charge on January 24, violent attacks have increased since March.
In the north and east, towns have been blockaded by insurgents who have blown up bridges and attacked supply convoys.
As in bordering countries, insurgents affiliated with Al-Qaeda and the Islamic State group have stoked unrest.
Thousands have died and about two million have been displaced by the fighting since 2015 when the insurgency spread to Burkina Faso, which has since become the epicentre of the violence across the Sahel.
In September, a particularly bloody month, Damiba sacked his defence minister and assumed the role himself.
Earlier this week, suspected jihadists attacked a convoy carrying supplies to the town of Djibo in the north of the country. The government said 11 soldiers died and around 50 civilians were missing.