The campaign group sent a letter to Pope Francis and Catholic leaders stressing the need for a low-carbon energy future.
"Your acknowledgement of the dire threat of climate change, the Vatican's efforts to become the first carbon-neutral state, and your dedication to caring for creation give us great hope," the letter states. "We urge you to use the power of your office to set an example for the world."
The organization provided no data on what portion of the investments in the Vatican Bank were in the fossil fuels sector. With $8 billion in holdings, 350.org said the bank's money was "inevitably" tied to energy companies.
Pope Francis himself has spoken out about the threat of climate change and Jamie Henn, a spokesman for 350.org, said it was time for the pontiff to take concrete action.
"We urge him to take appropriate steps to stop the Catholic Church from fueling the climate crisis through its investments, and use the power of his office to call on Christians and non-Christians alike to align their investments with their values," he said.