The pontiff said that the faiths have no choice but to come together to prevent "barbarous" attacks.
In April al-Shabaab claimed responsibility for an attack on a mostly Christian college in north-eastern Kenya that left 150 people dead, while in March al-Shabaab claimed responsibility for attacks in Mandera county on the Somali border in which 12 people died.
And in September 2013, at least 67 people were killed in an attack by al-Shabaab on the Westgate shopping centre in the capital Nairobi.
The Pope said that "all too often, young people are being radicalised in the name of religion to sow discord and fear, and to tear at the very fabric of our societies."
He continued saying that interfaith dialogue is not a luxury, but "essential".
Later he will celebrate Mass at a university campus and deliver a major speech on the environment.
Kenya, a former British colony, is mostly Christian. Muslims represent about 10% of the population.
"Here, I think of the importance of our common conviction that the God whom we seek to serve is a God of peace," the Pope said.
"How important it is that we be seen as prophets of peace, peacemakers who invite others to live in peace, harmony and mutual respect."
Listen to Premier's Hannah Tooley speak to Dominic Burbidge, a Catholic Voice on the issue and lecturer on African Studies at Oxford University here:
