Repairs to the crumbling structure of the main courtyard of the mosque and its surrounding rooms were carried out in three phases, spanning a period of four months, before the end of the year 2007. The project entailed the stripping off of the old crumbling walls throughout the courtyard, the addition of various reinforcements to the walls and ceilings, as well as maintenance on the electrical wirings throughout the mosque. Once the inner structure was completed, the floors and walls were then plated in various kinds of marble. Updates to the cooling units of the mosque began in late 2008, and new water filtration units were installed on November 28, 2008.
Construction work on the new ladies entrance to the mosque (Bāb al-Fatimah) began in late 2008, along with the construction work for new rooms to the mosque meant for serving refreshments to pilgrims.
Among the earliest of repairs done to the mosque after the fall of the regime of Saddam Hussein, were repairs done to one of the entrance gates of the mosque known as Bāb al-Qiblah. The gate and the outer wall had to be entirely refurbished due to the severe neglect they had withstood, and took seven months to complete, having started in early September, 2006.