He was born in Chiclana de la Frontera to Mariana Martínez Garillo and Agustín Muñoz Rodríguez, a soldier and municipal judge.
In 1934, he was elected to the Consejo Nacional de Izquierda Republicana' (National Council of the Republican Left) constituent assembly.
The DGS building was largely empty, Muñoz regarded the security forces as unreliable and political parties and unions were independently arranging searches, arrests, and killings.
Tribunals with inexperienced staff were held but when those convicted were imprisoned, they were often later taken from prison and executed by criminals of the same lawless checas that the CPIP was means to replace but now carrying DGS authorisation.
Muñoz spoke to the leaders of the Confederación Nacional del Trabajo (CNT), the anarchosyndicalist trade union group, to try to get help to impose some order but failed.
He then organised two armed groups mostly staffed by 'Assault Guards' of the Cuerpo de Seguridad y Asalto under CPIP auspices, nominally under his control, known as Los Linces de la Republica ('the Lynxes of the Republic') in the royal palace and the Escuadrilla del Amanecer ('Dawn Squad') operating from the DGS and more directly linked to Muñoz.
During this period, when his home town Chiclana was besieged by rebels, Muñoz's father was ordered to leave government buildings by es:Mariano Zapico, the civil governor (who was executed on 6 August).
[4]: 270 On 12 August, another trainload of prisoners was stopped by anarchists at Santa Catalina Vallecas; they uncoupled the train and set up three machine guns.
Muñoz later claimed that he was not informed of the plan to transport prisoners on 11 August and said that he allowed the Guardia Civil to leave to avoid forces of order being seen to be overwhelmed by armed civilians.
In the afternoon, the cabinet of prime minister Francisco Largo Caballero agreed to move to Valencia as it was expected Madrid would fall to the Nationalist rebels.
It is unclear if Muñoz or his deputy, the police chief Vicente Girauta Linares, had signed the original orders or if Muñoz had simply drawn them up, but in the chaotic environment that followed, a spate of sacas followed Serrano Poncela's signed orders, with Poncela under the overall direction of Santiago Carrillo and his deputy José Cazorla Maure.
Muñoz's acquiescence in the face of armed groups led to him being described as "passive" or even involved, though some argue he was not sufficiently supported by his more-senior colleagues, Pozas and Galarza.
Muñoz learned of the murder of his father by Nationalists and the death of his 16-year-old son, Manolo, who succumbed to pulmonary tuberculosis after 11 months in the Prisión Provincial de Sevilla.
The ship did not dock, but the remaining family was exchanged for a sister of Nationalist general Gonzalo Queipo de Llano and the children of the marquesses of Larios.
He was accused of being involved in the Paracuellos massacres and other killings of right-wingers and of being a "masón de alto grado" - a high-degree freemason, which was true.