After the events of October 2000, the IDF prohibited Israeli access to the tomb. As a result of Operation Defensive Shield, Nablus was reoccupied by the IDF in April 2002, with severe damage to the historic core of the city, where 64 heritage buildings suffered serious damage or were destroyed. Some Breslov hasidim and others began to take advantage of the new circumstances to visit the site clandestinely under the cover of darkness, evading army and police checkpoints. Eventually Joseph’s tomb was once more open to visits. In May 2002, Israeli soldiers mistakenly opened fire on a convoy of settlers taking advantage of an ongoing incursion in Nablus to visit the tomb. Seven settlers were arrested by the army for illegally entering a combat zone. As a result of Operation Defensive Shield, the tomb was retaken by the IDF and shortly afterwards, in response to numerous requests, they renewed guarded tours of the tomb. One day every month at midnight as many as 800 visitors were allowed to pray at the gravesite. These visits were designed to prevent unauthorized and unprotected clandestine visits, mainly by Breslav Hassidim. However, in October, citing security reasons, Israel re-imposed a ban on Jewish pilgrims obtaining special permits and travelling to the tomb.
In February 2003 it was reported in the Jerusalem Post that the grave had been pounded with hammers and that the tree at its entrance had been broken; car parts and trash littered the tomb which had a "huge hole in its dome." Bratslav leader Aaron Klieger notified and lobbied government ministers about the desecration, but the IDF said it had no plans to secure or guard the site, claiming such action would be too costly.
In February 2007, thirty five Knesset members (MKs) wrote to the army asking them to open Joseph's Tomb to Jewish visitors for prayer. In May 2007, Breslov hasidim visited the site for the first time in two years and later on that year, a group of hasidim found that the gravesite had been cleaned up by the Palestinians. In the past few years the site had suffered from neglect and its appearance had deteriorated, with garbage being dumped and tires being burned there.
In early 2008, a group of MKs wrote a letter to the Prime Minister asking that the tomb be renovated: "The tombstone is completely shattered, and the holy site is desecrated in an appalling manner, the likes of which we have not seen in Israel or anywhere else in the world." In February, it was reported that Israel would officially ask the Palestinian Authority to carry out repairs at the tomb, but in response, vandals set tires on fire inside the tomb. In December 2008, Jewish workers funded by anonymous donors painted the blackened walls and re-built the shattered stone marker covering the grave.
As of 2009, monthly visits to the tomb in bullet-proof vehicles under heavy IDF protection are organised by the Yitzhar based organization Shechem Ehad. In late April 2009, a group of Jewish worshipers found the headstone smashed and swastikas painted on the walls, as well as boot prints on the grave itself.
In August 2010, it was reported that the IDF and the Palestinian Authority reached an agreement on renovating the site. Israel's chief rabbis, Yona Metzger and Shlomo Amar, visited and prayed at the tomb along with 500 other worshippers, the first such visit by a high-ranking Israeli delegation in 10 years.
On April 24, 2011, Palestinian Authority police officers opened fire on three cars of Israeli worshipers after they finished praying at Joseph's Tomb. An Israeli citizen was killed and three others were wounded. The fatality was identified as Ben-Joseph Livnat, 25, the nephew of Culture Minister Limor Livnat. Both the Israel Defense Forces and Palestinian Authority ordered investigations into the incident. According to an initial investigation, three cars full of Israelis entered the compound of Joseph's Tomb without coordination with the Israeli military or Palestinian security forces and then tried to break through a Palestinian Authority police checkpoint. The IDF investigation concluded that the Palestinian police officers had acted "maliciously" and with the intent to harm the Jewish worshipers. IDF Chief of Staff Benny Gantz added that they fired "without justification and with no immediate threat to their lives."