Voter turnout in the local and parliamentary elections could be low – especially in pro-opposition neighbourhoods of the capital, Bujumbura.
Few voters could be seen at polling stations in areas like Ngarara, according to Katrin Wittig, a conflict resolution researcher who toured the area in the morning.
“We didn’t see many people voting,” she said. “Actually many of the people we saw voting were police or military.”
Some voters quickly tried to wash off the electoral marking stain indicating that they had cast their ballot. “They were afraid [...] that this could endanger them security-wise if people can see that they voted,” explained Wittig.
Some Ngarara voters received death threats to ensure that they would stay at home, according to presidential spokesperson Willy Nyamitwe. He refrained however from identifying the culprits in a Twitter message.
The voting nonetheless went smoothly apart from delays due to the violence, election commission spokesman Prosper Ntahorwamiye told AFP.
So-called “satellite parties” that enjoy close ties with the ruling CNDD-FDD party have fielded candidates.
But many opposition parties have pulled out from the race, calling for a boycott backed by civil society groups who allege the elections will be a “sham”.
There are concerns that the poll may trigger more protests and more repression, sending Burundi in a dangerous downward spiral.
“We have learned from very recent past that post-election violence can happen when elections are held in a very controversial manner,” Vital Nshimirimana, a civil society leader, said in an interview. “We know what happened in Kenya. This is our fear.”
UN Secretary General Ban Ki-Moon had called on Burundi to postpone the elections.
The decision to hold them nonetheless was condemned by the European Union on Monday.
"The organisation of legislative elections [...] can only exacerbate the profound crisis which is gripping Burundi," a spokeswoman for the EU diplomatic service said in a statement.
The African Union has refused to send observers to the polls. "The necessary conditions are not met for the organisation of free, fair, transparent and credible elections," AU chief Nkosazana Dlamini-Zuma said in a statement.
Opponents say Nkurunziza’s bid for another term violates the Arusha peace accord that paved the way to end 13 years of civil war in 2006.
At the weekend, parliamentary speaker Pie Ntavyohanyuma fled to Belgium, denouncing Nkurunziza's "illegal" bid to seek a third term. Presidential polls are due on 15 July.
Second vice-president Gervais Rufyikiri as well as election commission members and a constitutional court judge have also defected.
Some observers fear that Nkurunziza’s decision to run roughshod over the constitutional article setting a cap on term limits may lead him to scrap articles setting ethnic quotas in parliament.
Parliament must be made up of 60 per cent from the majority Hutu people -- who make up some 85 per cent of the population -- with the remaining 40 per cent of elected seats reserved for the minority Tutsi.
“People are obviously very concerned that if the two-term limit goes, what else could be subject to constitutional change?” explained Burundi watcher Cara E. Jones, a US academic.
There is an underlying fear that Burundi may once again descend into war.
Fearing for their lives, more than 120,000 Burundian citizens have already sought shelter abroad.
“Given my work as a lawyer and a civil-society activist I cannot stay in Burundi for my security,” confided Audace Gatavu, a Burundian lawyer who ran to Rwanda.
Like other Burundians abroad, he has not been able to vote. He didn’t want to cast his ballot anyway.
“The electoral commission that organised the election is not independent,” he remarked. “The situation that is prevailing in my country cannot allow me to vote. I would boycott the poll if I was in Burundi.”
Follow Michel Arseneault on Twitter @miko75011