On his first full day in Africa, Francis insisted that religion can never be used to justify violence and lamented 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 said interfaith dialogue isn't a luxury or optional, but is simply "essential."
On Friday, he heads to Uganda for the second leg of his first African pilgrimage.
Kenya, a former British colony is majority Christian, but Muslims represent about 10 per cent of the population.
In his remarks, Francis referred explicitly to three recent attacks claimed by the Somalia-based al-Shabab extremist group, saying he knew well that the memories were still fresh in Kenya's mind.
A month earlier, al-Shabab claimed responsibility for attacks in Mandera county on the Somali border in which 12 people died.
In September 2013, at least 67 people were killed in an attack by al-Shabab on the Westgate mall in Nairobi.
Al-Shabab opposes Kenya's decision to send troops to Somalia to fight the group as part of an African Union force backing Somalia's weak federal government.
"Here, I think of the importance of our common conviction that the God whom we seek to serve is a God of peace," Francis 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."
He said Christians and Muslims must work together to accommodate one another, and lead the country. "We should not step back," he said. "We have to lead, because we are led by the word of God.
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