Steve Fainaru, interim editor-in-chief of The Bay Citizen

Fainaru's exit comes at a time of extreme transition for the nonprofit news organization. In September, the company's founding editor-in-chief, Jonathan Weber, left the organization for Reuters. The following month, its CEO, Lisa Frazier, announced she would stepping down as chief executive.

Last month, the organization's founder, the philanthropist Warren Hellman, who launched the organization with $5 million in seed money in 2009, died at age 77 of complications from treatment for leukemia.

In an interview, Fainaru said he was grateful for his time at The Bay Citizen and said he was "honored to be part of an effort to try to solve problems and create opportunities and do good journalism."

Fainaru said that despite the turmoil, he remains optimistic about The Bay Citizen's future. The organization is currently hiring reporters and editors, he said, and will continue to grow.

"Proportionally, we are hiring more people than any other news outlet in the country," he said.

Frazier said, "Steve has done a great job as an editor and we wish him well."

"The Bay Citizen started with strong founding principles and has a great team and is confident in its future," she said.

She said the organization has raised $17.5 million since its inception, with $6 million of that coming from Hellman.

Frazier's last day is Feb. 6. Fainaru's last day is Feb. 9. Their replacements have not been named.