The pope and Guterres met privately for about 40 minutes in the papal library.
Francis denounced nuclear weapons, repeating his position that the mere possession of nuclear weapons is immoral, and Guterres praised the pope's disarmament efforts.
Two years ago, nearly two-thirds of United Nations states agreed to a treaty to ban nuclear weapons but the talks were boycotted by the United States, France, Britain and others.
Guterres called on nations to commit to carbon neutrality by 2050, "in line with what the scientific community tells us is necessary to rescue the planet".
He spoke five days after a U.N. climate summit in Madrid closed with major states snubbing calls for tougher action to combat global warming, prompting sharp criticism from smaller countries and environmental activists.
Both spoke of the need for inter-religious dialogue and condemned the concept of violence in God's name.
"Tragically we see Jews being murdered in synagogues, their gravestones defaced with swastikas; Muslims gunned down in mosques, their religious sites vandalised; Christians killed at prayers, their churches torched," Guterres said."We need to do more to promote mutual understanding and tackle rising hatred," he said.