Pope Francis left Kenya at 3.51pm on Friday after a three-day visit whose last day included a compelling warning against 'sweet' corruption.
President Uhuru Kenyatta, DP William Ruto, First Lady Margaret, Senate Speaker Ekwee Ethuro and several senior government officials saw him off at the JKIA.
Francis held a private meeting with Catholic leaders before leaving for the airport where traditional dancers entertained him and the Kenya Defence Forces band performed.
He shook the hands of Catholic leaders and boarded the 'Shepherd One' Alitalia flight alongside four Kenyan journalists who will return after his arrival in Uganda.
The Uganda visit is the second leg of the Pope's maiden tour of Africa that will end in the Central African Republic.
Francis' characteristic humility during his time in Nairobi endeared him to the public who criticised leaders over their use of expensive guzzlers unlike the simple vehicles he rode in.
His messages during a Mass and meetings with religious leaders and the youth emphasized a joint war against corruption, strong family units, reconciliation and bridging the gap between the rich and the poor.
Thousands attended the Thursday Mass at the University of Nairobi despite the rain, cold and muddy. At Safaricom Stadium Kasarani on Friday, some members of the public arrived as early as 5am.
Pope Francis went off script in his address at Kasarani saying corruption was not beneficial as it "eats from the inside" and results in a vicious cycle after the death of perpetrators who stole property.
"The spirit of evil takes us to a lack of unity. It takes us to tribalism, corruption and drugs. It takes us to destruction out of fanaticism," he said, urging young people not to give in to these vices.
"Let's hold hands together, let's stand up as a sign against bad tribalism," he further said, grasping the hands of two young people on stage.
He also addressed landgrabbing, "a sin against humanity' saying he knew about "faceless private developers who even attempt to appropriate the playgrounds of your children’s schools".
Francis' visit to Kangemi slum was also a highlight. He said he is concerned about the plight of those living in the slum, which he described as "wounds" resulting from inequality.
In Uganda, the Pope will visit Namugongo and the forgotten Munyonyo shrines, in honour of slain martyrs including St Andrew Kaggwa the patron of catechists in the country.
He will be the third pontiff to tour Uganda where his key agenda is visiting the shrines. The trip to the country comes after the 50th anniversary of the martyrs.
The 45 Ugandan Martyrs were killed by Kabaka Mwanga of Buganda between 1886-1887 for refusing to recant their faith - 23 were Anglican and 22 Catholic.
Francis had been invited to the national Uganda Martyrs Day that more than three million pilgrims attended on June 3 but did not make it.