The pope will revisit the themes raised during the synod of African bishops in 2009, when he had called for peace, reconciliation and justice.
The continent has the world's fastest growing number of Catholics - rising by eight million between 2007 and 2008 alone - and often sends its dynamic priests to work in increasingly deserted churches across the secularised West.
But the African Church is also riddled with scandals, from child abuse to extramarital relations, collusion with those in power, and ill-gotten fortunes.
African priests have also been known on occasion to be involved with practices that do not sit happily with the Catholic Church - from exorcism or animal sacrifices to Freemasonry.
In Benin alone, two bishops - including the Archbishop of Cotonou Marcel Honorat Agboton - have been dismissed for sex and corruption scandals.
Ahead of his three-day visit, Benedict has denounced ritual killings in witchcraft practices - a widespread problem in Africa where albinos are often singled out.
The pontiff has also asked those involved in conflicts, such as the strife dividing the Ivory Coast since 2002, not to be afraid to shed light on crimes committed.
He recently called for a cessation to violence between Christians and Muslims in Nigeria, where radical Salafists rival mainstream Islam.
The Church "does not want to be a substitute for the state, but can - through its numerous institutions in the education and health sectors - bring comfort and care", he said.
Rural depopulation and the promotion of an identity beyond ethnic borders in Africa is seen as a chance for the Catholic Church to reinforce its role as "protector of the weak".
It also hopes to become a "new family" for many, stepping into the void left by weakening community structures, said Mario Giro from the Sant'Egidio community - a Catholic group active in peace-building initiatives in Africa.
According to a Vatican source, the Church feels it has a duty to help Catholics develop a "true conscience" in a region where bad governance abounds.
Competition among religions is fierce in this poverty-struck region.
Many disappointed Catholics have converted to Pentecostalism, which "offers the full package, while the Church only offers a few Hail Marys", said a Beninese religious commentator.
"We need a second evangelism, which would help those baptised not to allow themselves to be attracted by those selling illusions," said Father Ballang, head of the French-speaking African department at the Vatican Radio.
In the meantime the Church is dedicating a lot of its time to improving education and is the main institution engaged in caring for those with Aids, even though it is officially opposed to the use of condoms.
Benedict's first visit to Africa in 2009 was overshadowed by a controversial comment when he said the distribution of condoms "aggravates" the Aids crisis and spoke of sexual abstinence as the only solution.