Upon the assassination of his father in 1002, Eckard II and his elder brother Herman I ruled over the Ekkeharding allodial lands, while the Meissen margravial title first passed to their uncle Gunzelin feuding with his nephews until his deposition in 1009.

With the consent of Emperor Conrad II, he and his brother Herman had the seat of the Bishopric of Zeitz relocated to Naumburg Cathedral in 1028–29.

As guardian of the German eastern frontiers against Poland and Bohemia, he was often serving Emperor Conrad II and his successor King Henry III against these menaces, including the "Bohemian Achilles", Duke Bretislaus I.

In 1039 Bretislaus, allied with King Peter of Hungary, who was at the same time raiding the Bavarian Avar March, made great gains in Poland, plundering Kraków and Gniezno, where he took along the relics of Saint Adalbert of Prague.

In turn, King Henry III launched a campaign against him, together with his loyalest and most trusted allies, Archbishop Bardo of Mainz and Margrave Eckard.