During the reign of Askia Dawud of the Songhai Empire, Djinguereber mosque was renovated by the Qadi of Timbuktu Aqib ibn Mahmud beginning in 1570.

[6] On 26 February 2010, during Mawlid (a festival to mark the birth anniversary of Muhammad), a stampede at the mosque killed around 26 people and injured at least 55 others, mostly women and children.

[7] On 1 July 2012, militant Islamists of the Ansar Dine ("defenders of faith") began destroying the tombs of Timbuktu shortly after UNESCO placed them on a list of endangered World Heritage sites.

[10] A four-year project towards the restoration and rehabilitation of the Mosque began in June 2006, and is being conducted and financed by the Aga Khan Trust for Culture.

This work included drainage and paving around the mosque, re-rendering walls in bad condition and in one zone of the roof, replacing around 50% of the beams, above which was a heavy build-up of mud plaster.

The local masons in charge of the project clearly had good technical expertise; however, there is a need to regularly document their activities and starting point.