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Imprisonment: 1954–1961

During the appeal process, a prison had been built at Lokitaung, where Kenyatta and the four others were then interned. The others were made to break rocks in the hot sun but Kenyatta, because of his age, was instead appointed their cook, preparing a daily diet of beans and posho. In 1955, P. de Robeck became the District Officer, after which Kenyatta and the other inmates were treated more leniently. In April 1954, they had been joined by a captured Mau Mau commander, Waruhiu Itote; Kenyatta befriended him, and gave him English lessons. By 1957, the inmates had formed into two rival cliques, with Kenyatta and Itote on one side and the other KAU members—now calling themselves the "National Democratic Party"—on the other. In one incident, one of his rivals made an unsuccessful attempt to stab Kenyatta at breakfast. Kenyatta's health had deteriorated in prison; manacles had caused problems for his feet and he had eczema across his body.

Kenyatta's imprisonment transformed him into a political martyr for many Kenyans, further enhancing his status. A Luo anti-colonial activist, Jaramogi Oginga Odinga, was the first to publicly call for Kenyatta's release, an issue that gained growing support among Kenya's anti-colonialists. In 1955, the British writer Montagu Slater —a socialist sympathetic to Kenyatta's plight—released The Trial of Jomo Kenyatta, a book which raised the profile of the case. In 1958, Rawson Macharia, the key witness in the state's prosecution of Kenyatta, signed an affidavit swearing that his evidence against Kenyatta had been false; this was widely publicised. By the late 1950s, the imprisoned Kenyatta had become a symbol of African nationalism across the continent.

His sentence served, in April 1959 Kenyatta was released from Lokitaung. The administration then placed a restricting order on Kenyatta, forcing him to reside in the remote area of Lodwar, where he had to report to the district commissioner twice a day. There, he was joined by his wife Ngina. In October 1961, they had another son, Uhuru, and later on another daughter, Nyokabi, and a further son, Muhoho. Kenyatta spent two years in Lodwar. The Governor of Kenya, Patrick Muir Renison, insisted that it was necessary; in a March 1961 speech, he described Kenyatta an "African leader to darkness and death" and stated that if he were released, violence would erupt.

This indefinite detention was widely interpreted internationally as a reflection of the cruelties of British imperialism. Calls for his release came from the Chinese government, India's Nehru, and Tanganyika's Prime Minister Julius Nyerere. Kwame Nkrumah—whom Kenyatta had known since the 1940s and who was now President of a newly independent Ghana—personally raised the issue with British Prime Minister Harold Macmillan and other UK officials, with the Ghanaian government offering Kenyatta asylum in the event of his release. Resolutions calling for his release were produced at the All-African Peoples' Conferences held in Tunis in 1960 and Cairo in 1961. Internal calls for his release came from Kenyan Asian activists in the Kenya Indian Congress, while a colonial government commissioned poll revealed that most of Kenya's indigenous Africans wanted this outcome.

By this point, it was widely accepted that Kenyan independence was inevitable, the British Empire having been dismantled throughout much of Asia and Macmillan having made his " Wind of Change " speech. In January 1960, the British government made its intention to free Kenya apparent. It invited representatives of Kenya's anti-colonial movement to discuss the transition at London's Lancaster House. An agreement was reached that an election would be called for a new 65-seat Legislative Council, with 33 seats reserved for black Africans, 20 for other ethnic groups, and 12 as 'national members' elected by a pan-racial electorate. It was clear to all concerned that Kenyatta was going to be the key to the future of Kenyan politics.

After the Lancaster House negotiations, the anti-colonial movement had split into two parties, the Kenya African National Union (KANU), which was dominated by Kikuyu and Luo, and the Kenya African Democratic Union (KADU), which was led largely by members of smaller ethnic groups like the Kalenjin and Maasai. In May 1960, KANU nominated Kenyatta as its president, although the government vetoed it, insisting that he had been an instigator of the Mau Mau. KANU then declared that it would refuse to take part in any government unless Kenyatta was freed. KANU campaigned on the issue of Kenyatta's detainment in the February 1961 election, where it gained a majority of votes. KANU nevertheless refused to form a government, which was instead created through a KADU-led coalition of smaller parties. Kenyatta had kept abreast of these developments, although he had refused to back either KANU or KADU, instead insisting on unity between the two parties.