In 1534 Murat Reis accompanied Hayreddin Barbarossa to Constantinople where they were received by Suleiman I and appointed to take command of the Ottoman fleet.

On September 25 and 26, 1538, he was assigned with the task of preventing the ships of the Holy League under the command of Andrea Doria from landing at Preveza, and he successfully repulsed them from the shoreline.

Murat Reis was later assigned with the task of controlling the lucrative trade routes between Egypt and Anatolia which were often raided by the Venetians, the French and the Maltese Knights.

In 1609, he heard of the presence of a joint French-Maltese fleet of ten galleys, including the famous Galeona Rossa, a large galleon armed with 90 cannons which was known among the Ottomans as the Red Inferno, under the command of a knight named Fresine, off the island of Cyprus, and sailed there to engage them.

One of the municipalities that form the City of Algiers, which was once the regional capital of the Ottoman Eyalet of Algeria (1517–1830), is named Bir Mourad Raïs (Murat Reis' well) in his honor.