Godfrey rebelled against his king and devastated land in Lower Lorraine, as well as the city of Verdun, which, though his by inheritance, Henry had not given him. He was soon defeated by an imperial army and was deposed imprisoned together with his son (Gibichenstein, 1045). When his son died in prison, the war recommenced. Baldwin V of Flanders joined Godfrey and Henry gave Thierry, Bishop of Verdun, the eponymous county. Godfrey surprised the bishop (who escaped) and sacked Verdun, burning the cathedral. On 11 November 1048 at Thuin, Godfrey fell on Adalbert, his replacement in Upper Lorraine, and defeated him, killing him in battle. Henry immediately nominated the young Gerard of Chatenoy to replace Adalbert at the Diet of Worms. In his subsequent campaigns to take the Moselle region, Godfrey met with stiff resistance from Gerard and was forced to renounce his claims and reconcile with the bishop. He even assisted in rebuilding the cathedral he had destroyed.
In 1053, his first wife Doda having died, Godfrey remarried to Beatrice of Bar, the widow of Boniface III of Tuscany and mother of Matilda, Boniface' heir. Henry arrested Beatrice and her young son Frederick and imprisoned her in Germany, separate from either husband or son, who died within days. The emperor claimed the marriage had been contracted without his consent and was invalid. Young Frederick died a short while later. Nevertheless, Godfrey took over the government of the Tuscany in right of Beatrice and Matilda.
Baldwin V then rebelled, carrying the war to Trier and Nijmegen. Henry responded by devastating Flanders and ravaging Lille and Tournai (1054). In this war, Godfrey captured Frederick of Luxembourg, Duke of Lower Lorraine, who had received that duchy, including Antwerp, from Henry III.
In 1055, Godfrey besieged Antwerp, but Frederick was delivered by the Lorrainers, no longer loyal to Godfrey. Henry died in 1056 and his successor, Henry IV, was only six years old. In that year, Baldwin made peace and did homage to the new king. In 1056 and 1059, by the treaties of Andernach, Baldwin received the march of Ename in the Landgraviate of Brabant, probably in exchange for giving up the march of Valenciennes, which was confiscated by emperor Henry III in 1045.
In 1057, Godfrey was exiled to Tuscany, where he joined Beatrice and co-governed with her. He was enfeoffed with the Duchy of Spoleto (1057) by Pope Stephen IX, his brother. In January 1058, Leo de Benedicto Christiano threw open the city gates to him and Beatrice after the election of Pope Nicholas II. Possessing the Tiber and assaulting the Lateran, Godfrey succeeded in expelling the antipope Benedict X on 24 January. During the papal reign of his brother and his brothers reforming successors, he played an important rôle in the politics of central and northern Italy, including Sardinia, where he interfered on behalf of Barisone I of Logudoro against the Republic of Pisa, indicating his authority over both.