In early 1934, Hitler and other Nazi leaders became concerned that Ernst Röhm, chief of the SA, was planning a coup d'état. Hitler decided on 21 June that Röhm and the SA leadership had to be eliminated. The purge of the SA leadership and other enemies of the state began on 30 June in an action which became known as the Night of the Long Knives. Eicke, along with hand-chosen members of the SS and Gestapo, assisted Sepp Dietrich's Leibstandarte SS Adolf Hitler in the arrest and imprisonment of SA commanders, before they were shot. After Röhm was arrested, Hitler gave the order that the imprisoned Röhm was to be executed. Himmler communicated Hitler's order to Eicke. Eicke was told to first give Röhm the choice to commit suicide. Accompanied by Lippert, and SS-GruppenführerErnst-Heinrich Schmauser, Eicke travelled to Stadelheim Prison in Munich where Röhm was being held. After telling Röhm that he had forfeited his life and that Hitler had given him a last chance to avoid the consequences, Eicke laid a pistol on a table in Röhm's cell and told him that he had 10 minutes in which to use the weapon to kill himself. Eicke, Lippert and Schmauser left and waited in the corridor for 15 minutes, during which time no shot was heard. Finally, Eicke and Lippert drew their pistols and re-entered Röhm's cell. Both fired and Röhm fell to the floor. One of the two then crossed to Röhm and administered a coup-de-grace.
In 1956, the Munich authorities began an investigation into the Night of the Long Knives and in August arrested Lippert and Sepp Dietrich for their part in it. They were bailed, and the trial itself did not commence until 6 May 1957. They were represented by the lawyer Alfred Seidl who had defended Rudolf Hess at the Nuremberg Trials. Lippert and Dietrich were charged with manslaughter, in Lippert's case for the death of Röhm. Lippert asserted that he had remained outside Röhm's cell, and only Theodor Eicke had gone in. On 10 May, the case was summed-up and the prosecutor demanded a two-year sentence for Lippert. On 14 May, the President of the Court found both Lippert and Dietrich guilty and sentenced both men to 18 months. He described Lippert as "filled with a dangerous and unrepentant fanaticism". Lippert died on 1 September 1969.