The forced departure of Malian President Ibrahim Boubacar Keita, known as IBK , has already prompted fears that jihadis with strongholds in northern Mali could carry out attacks on vital facilities and further destabilize the country.
Terror groups with links to al-Qaida and "Islamic State" could take advantage of the current leadership vacuum too, observers are warning.
"The political situation after the military coup in Bamako is, unfortunately, a lot worse than it was before. Now, we have a military coup, and the crisis in Bamako will also have a significant impact on the security situation in the entire region of the Sahel," Thomas Schiller, of the Konrad Adenauer Foundation in the Malian capital, Bamako, told DW.
"There were massive demonstrations against the president in the preceding weeks, supported by a protest movement called M5-RFP: This protest movement contributed to the fact that there was already a sociopolitical crisis in Bamako," Schiller added.
Keita 'failed to read the signs'
Keita's forced resignation came after months of a political crisis that stemmed from a disputed parliamentary election. In June, anti-government protesters took the streets of the capital demanding Keita's step down. He remained largely defiant, but in early July attempted to appease the opposition. However, the movement's leaders insisted that he resign and parliament be dissolved, as well as urged civil disobedience.
"Keita and the people around him failed to read the signs correctly, and the president's lack of understanding ignited the masses," Schiller said.
"Many Malians think he wasn't doing enough to stabilize the country and end growing corruption in the country," he added. "So, there were a lot of very disappointed Malians."
Mali has been among the top 10 countries of origin for migrants arriving in Europe via Italy. In October 2016, German Chancellor Angela Merkel pledged to support the government in Mali in bringing about stability and development.
"Development cooperation must be strengthened next year in all parts of Mali's northern region," Merkel said at the time. She had suggested that this could help with stability and, therefore, also prevent migration.
ECOWAS missed an opportunity
At the height of demonstrations in mid-June, the Economic Community of West African States (ECOWAS) called for the creation of a "consensus government of national unity."
None of the parties was willing to make concessions, which brought the mediation to a standstill.
The coalition led by popular cleric Mahmoud Dicko accused Keita's administration of "bad governance and non-governance" at the end of the talks. At the same time, a spokesperson for Keita's camp described the calls for the president's resignation as unconstitutional.
According to Schiller, although mediation efforts by ECOWAS leaders were an important step to bring both parties together, they were not good enough to address the concerns as laid out by Mali's opposition.
"The opposition was always firm on its demands, and perhaps the mediators should have been more understanding to the protestors' demands," Shiller said, adding that the government made enormous mistakes and was becoming unpopular.
"We know that both presidential and the parliamentary elections were not very credible, and the outcome is something the government underestimated," he said.
A torpedoed peace deal
Brema Ely Dicko, a sociologist in Bamako, told DW, "I am not surprised [by the coup], the resentment within the army, and the UN report [which has been submitted to the UN Security Council but is not yet public ] accuses senior military officers close to the regime of torpedoing the Algiers peace treaty."
The Algiers peace treaty is a peace and reconciliation agreement that was signed in 2014 between the government of Mali and warring factions in northern Mali, known by some as Azawad.
Niger's foreign minister, Kalla Ankourao, told DW the latest developments in Mali were disappointing. Ankourao is part of the ECOWAS mediation team, which Niger currently chairs.
"For us, this is a disappointment! For two months we tried to mediate and hoped that the Malian people would adhere to the ECOWAS guidelines, that is democracy and good governance ... That [the coup] was a brutal stop of the negotiations," Ankourao said.
The 15-member regional bloc was unable to broker a solution and suspended Mali from its institutions as soon as the coup became apparent.
Religion's influence on politics
In recent years, the influence of religion on Malian society and politics has taken a foothold. The rising threats from Salafist jihadi groups based in the Sahel have made it difficult for Malian authorities, even with the support of foreign troops, to rein in outspoken clerics in the country.
Mahmoud Dicko, an imam viewed as the opposition's figurehead, on August 11 told protesters: "This combat is to restore the Malian nation ... If IBK doesn't listen to us, he will see. I swear before God that he will see. But if we don't rush, we will win this victory."
Mali's religious leaders draw crowds so large that they are the envy of politicians and celebrities. Dicko's influence has been obvious since June.
"Well, the moral figure in this whole process, in the process that led to the coup d'etat was an imam," Abdoulaye Sounaye, from the Leibniz Center for Modern Oriental Studies (ZMO), told DW.
"Imam Dicko was the one who claimed that something needed to change in Mali. What he said was when Ibrahim Boubacar Keita was preparing for his campaign in 2013, he helped him to get elected. He helped him again to a second term, but now he's fed up."
Foreign troops on high alert
The international community quickly condemned the coup in the country, which was already struggling to contain an insurgency that claimed thousands of lives in 2012.
French and German troops stationed in the Sahel region are on high alert.
Mali is the linchpin of French-led efforts to roll back jihadis in the Sahel, and its neighbors are anxious to avoid the country sliding into chaos. Swathes of its territory are already outside of the government's control.
In May, the German Bundestag approved an extension of its troop deployment in Mali until 2021 under a mandate to fight militants in the Sahel, a situation one politician described as "very acute" across the region.
Schiller said the international community plays a significant role, and it cannot afford to pacify military leaders.
"It is a tragedy that this political crisis has escalated in Bamako and that every attempt to stabilize the country has now been thwarted," Schiller told DW.
"I hope that everyone in Mali becomes responsible, and a solution is found which has to be constitutional as soon as possible," he said. "The security crisis will not wait for the Malian politicians and members of the coup to solve."
Mali and Niger form part of the G5 alliance, a joint security operation with Burkina Faso, Chad, and Mauritania, aiming to fight terrorism and track terror suspects in the Sahel region.
Despite the presence of thousands of foreign troops in the country, insurgents have swept into central Mali, as well as into neighboring Burkina Faso and Niger. Frequent clashes with jihadis take place along the common borders of the three countries.
EU will insist on new elections
Both regional and international political players hope that the situation in Mali doesn't escalate into anarchy. On Wednesday, the African Union suspended Mali and called for an immediate return to civilian rule.
The European Union said it will insist on new elections within a reasonable timeframe. China said it opposes regime change by force.
ECOWAS, having previously warned it would no longer tolerate military coups in the region, said it plans to send a delegation to Mali to ensure a return to constitutional democracy.
"We have to see what happens in the next days. At some point it is very important that stability is brought back to Mali, which is already in a very difficult situation," Schiller said.
Uta Steinwehr contributed to this article.