The court ordered the arrest of those to be investigated, had them imprisoned at Jilava, and entrusted them to the custody of special Legionary formations, described by Alexandru Creţianu as "nothing less than an improvised version of the SS strong-arm squads".
The investigation underway, the court, wishing to obtain testimony from the detainees in order to prepare for their trials, ordered several of them to be transferred to another jail, where their depositions would be taken. However, Ştefan Zăvoianu, the Bucharest Prefect of Police in charge of the Legionary squads guarding the prisoners, believed Antonescu had changed his mind about executing those responsible for Codreanu's death and refused to comply with the order. This alerted the military authorities, who decided to replace the squads with regular military guards and move the prisoners themselves. Zăvoianu was informed of this decision on November 26, and that night the squads shot dead every one of their charges: politicians, senior military officers, and policemen accused of complicity in Codreanu's arrest and execution.
The execution team was commanded by Dumitru Grozea, head of the Legionary Workers' Corps. Its members were aged between 18 and 25. Gheorghe Creţu, who killed 14 inmates, testified at his trial that Grozea gave the order to shoot at around 11:45 pm, whereupon each executioner was sent to a particular cell, ordered the prisoners to stand and shot them. The executioners then gathered before the guards; together they went and paid homage before Codreanu's remains.
Among those assassinated were former Prime Minister Gheorghe Argeşanu (who had presided over the reprisals following Armand Călinescu's assassination), former Justice Minister Victor Iamandi, former Bucharest police prefect and interior minister Gabriel Marinescu, several high-ranking officers of the Gendarmerie, including its head inspector General Ion Bengliu, Colonel Zeciu (who had organised the killing of Codreanu and thirteen other Legionnaires), Majors Aristide Macoveanu and Iosif Dinulescu (who had prepared and carried out the killing), Staff Sergeant Sârbu (who had actually tightened the wire around Codreanu's neck, strangling him), Mihail Vârfureanu (a former Legionnaire who turned informant and was responsible for female Guardist Nicoleta Nicolescu's assassination), former Chief of Secret Police Mihail Moruzov, and his deputy. The last two were not responsible for excesses against the Iron Guard, but in the past they paid many of its members, including Codreanu's successor as leader, Horia Sima, for services rendered as informants. Zăvoianu knew that the Legion would like to be rid of such inconvenient witnesses before any trials or investigations could take place.
Sima replied that such a deed would not be repeated, to which Antonescu drew his attention to the fact that Nicolae Iorga's safety was threatened by Legionaries and he should take steps to ensure no harm was done.
Sima agreed, but by the end of the day was informed that Iorga, the venerable historian and former prime minister, had been murdered. Several Guard members had attacked him and Virgil Madgearu, secretary general of the National Peasants' Party, in their homes, kidnapped and shot them, and abandoned their bodies in a roadside ditch. Also on November 27, Zăvoianu and his men rounded up more leading figures of the Carlist regime, including former prime ministers Constantin Argetoianu and Gheorghe Tătărescu (saved by the quick intervention of Lt. Col. Alexandru Rioşanu), former prime minister Ion Gigurtu (saved by Sima) and former ministers Mihail Ghelmegeanu and Nicolae Marinescu; they were brought to the Police Prefecture with the intention of executing them, but spirited away to safety in the heavily fortified building of the Interior Ministry.
Codreanu, whose body was discovered on November 25, was solemnly reburied on November 30, along with the Decemviri and Nicadori. The Guard would claim that the assassins acted solely out of fury and a desire for revenge (the remains of their hero were being unearthed a short distance away as the massacre proceeded), and while the discovery doubtless stirred them to action, the procurement of arms and prison plans involved detailed planning that took time and premeditation. In July 1941, Zăvoianu, along with the former Legionary police officers Gheorghe Creţu, Octavian Marcu, Constantin Savu and loan Tănăsescu, and the Legionary Dumitru Anghel, were condemned to death and shot for perpetrating the massacre. That month, Dumitru Grozea and thirteen of his accomplices, mainly former police officers and Iorga's assassins, were condemned to death in absentia.