Army Captain Ibrahim Traore announced on Friday evening that he had ousted Burkina Faso's military leader, Paul-Henri Damiba, sparking a weekend of upheaval as violent protests broke out in the capital and two army factions battled for control.
Damiba offered his resignation on Sunday, with a list of conditions. He had ousted the country's previous president, Roch Kabore, in January for failing to contain an Islamist insurgency - the same reason Traore said he ousted Damiba.
Neighbouring Togo's government on Monday confirmed reports that Damiba was in the country, saying he was being hosted "in the spirit of peace".
Political instability in Burkina Faso could worsen disruption that rampant insecurity has already brought upon schools across the region, which are often targeted by militants.
More than 11,000 schools in the Central Sahel and the Lake Chad Basin are closed due to conflict or threats made against teachers and students, according to UNICEF.
Children across the region have missed out on their first day of school this year.
"It was an uncertain start to the school year but thanks to God, everything is going well. The atmosphere is good," said Weknouni Kabre, a teacher at Pissy primary school, where smiling students greeted their friends and lined up for roll call.
"With a little worry given the situation, our wish as parents is that things go normally," said Seydou Niampa, the father of two students at Pissy. "Since the authorities are reassuring us, we wish them good luck too with this first day."
Business had returned to usual throughout the capital on Monday, with bustling streets and stores reopened. But tensions remained.
Protests broke out over the weekend at the French embassy, after Traore's forces said Damiba had taken refuge at a French army base. France has denied any involvement in the events.
A few smaller, scattered protests were reported across the capital on Monday. One outside the French embassy was quickly broken up by military police, an embassy source said.
"We can't be 100% sure there won't be any disruptions. But we dare to believe that... we'll be able to start and complete the year in peace," said Edgard Zongo, director of the Pissy school.
(Reporting by Thiam Ndiaga; Additional reporting by Anne Mimault in Ouagadougou and Noel Kokou Tadegnon in Lome; Writing by Nellie Peyton; Editing by Sofia Christensen and Sandra Maler)