In this period, in collaboration with the theologian Valentino Salvoldi, he wrote a book calling for an African Synod, “Africa: the Gospel Belong to Us” which was later published also in Italian and Portuguese.
Once in Nairobi, he started a lay community in Kenya, also called Koinonia, with a group of young men whose inspiration was the life of the early biblical Christians as recorded in the Acts of the Apostles.
The present war has caused the closure of the project, but a secondary school in Yida refugee camp for the Nuba people in South Sudan is supported by Koinonia.
In a letter dated 31 August 1999 addressed “To whom it may concern”, Archbishop Paulino Lukudu Loro, the President of SCBC, wrote on behalf of the bishops: "It came to our knowledge that Father Kizito raises funds for the Nuba Mountains by presenting projects to church or church-related organisations.
Consequently he has no authorisation whatsoever to raise funds in our name and/or in the name of our respective dioceses... We are also concerned that in the past Father Kizito has issued public statements about the situation in Sudan.
We emphasise that he is not authorised by the Bishops to speak as the voice of Church..." Beyond his missionary and humanitarian work, Father Kizito is an acclaimed writer and journalist.
He wrote a weekly column called "Father Kizito's Notebook" from 1995 to 2001, in the Sunday edition of the Daily Nation, which is Kenya’s most widely read newspaper.
Father Kizito has also inspired and supported the establishment of Newsfromafrica.org, an electronic news bulletin that publishes articles written from the perspective of the African grassroots people in their struggle for freedom, dignity and justice.
At the end of 2015 Koinonia manages in Nairobi seven children and youth homes, a secondary school, two higher education institutions, two community radio stations, and Shalom House, a centre for justice and peace with modern residential facilities.
In Lusaka hosts in the same location a children and youth home, a secondary school, while a public library and an organic agricultural training centre are under construction.