After her commissioning in 1925, Emden was used as a training ship for naval cadets. She made a series of world cruises to show the flag in the pre-war period and trained large numbers of cadets.
In 1925–1926, a series of modifications were made to the ship, including increasing the height of the second funnel and the installation of a flying bridge at the base of the battle mast, which was shortened by 7.01 meters (23 feet). Lothar von Arnauld de la Perière commanded the ship from September 1928 until October 1930.
In April 1933, her coal-fired boilers were replaced with more efficient oil-fired boilers. The next year, another series of modifications was made, including reducing the main mast and funnels in height and the installation of a small crane on the starboard side of the main mast.
In September 1934, Karl Dönitz, the future commander of the Kriegsmarine, took command of the ship and remained in the position until September 1935. Emden went into dock for further modifications in 1936; the ship's masts were again reworked, and the third 8.8 cm anti-aircraft gun was added. Leopold Bürkner commanded the Emden from July 30th 1937 to June 15th 1938.