Three weeks after Flexport founder Ryan Petersen as CEO and returned to run his supply chain software startup, the company has ousted its chief financial officer, and its human resources chief has resigned, CNBC has learned.

Flexport informed CFO Kenny Wagers last week that he was being let go, according to people familiar with the situation. His last day is Friday.

Stuart Leung, Flexport's head of finance, is expected to be named CFO, said the people, who asked not to be named because they weren't authorized to speak publicly on the matter. Leung has worked at Flexport for seven years in various operations, logistics and finance roles, and is viewed as a close confidant of Petersen's.

Petersen, who founded Flexport a decade ago and built it into a Silicon Valley darling valued at $8 billion by prominent investors, at the company on Sept. 6, after he and the board forced Clark to resign. Clark, who spent 23 years at Amazon and became a top member of leadership team, was hired by Petersen a year ago, in part to help the company move towards an IPO, sources said.

Clark and Petersen worked as co-CEOs of Flexport starting last September, and Clark took over as the company's sole CEO in March. Petersen became a venture partner at Peter Thiel's Founders Fund, one of Flexport's top backers.

Jennifer Boden, Flexport's vice president of people tech and employee experience, is also leaving the company, the sources said. Boden took over the role earlier this month after her predecessor, Darcie Henry, was let go from Flexport.

A Flexport spokesperson confirmed the personnel moves, and said that Michael Brown will take on a new role as Head of Restructuring and CEO Initiatives, but declined comment on possible layoffs.

"Kenny Wagers made a tremendous impact at Flexport, and we are grateful for his contributions steering Flexport as one of the fastest-growing companies during his tenure. We wish Kenny the best as he pursues his next opportunities. Stuart Leung will become Flexport's Chief Financial Officer and report to Ryan Petersen, CEO, effective immediately. Stuart has been with Flexport for nearly seven years having held vital senior leadership roles in finance, sales, and operations. As CFO, he will focus on leading Flexport's return to profitability and growth.

"Michael Brown will take on the role of SVP, Head of Restructuring and CEO Initiatives. In this newly created role, he will focus on restructuring the business to be more customer-centric and leading our return to profitability. Jennifer Boden will be leaving Flexport to pursue new opportunities. We thank Jennifer for her leadership and wish her all the best in her future endeavors."

Petersen has fired many of the executives Clark recruited from Amazon, including Henry, as well as Teresa Carlson, who was the company's president; Tim Collins, who served as executive vice president of global operations; and Kelly Cheeseman, a vice president and chief of staff.

Flexport launched in 2013 as a digitally focused freight forwarder, and recently to become an end-to-end supply chain services company, fulfillment provider Deliverr from in May. In addition to Founders Fund, the company has also raised capital from Andreessen Horowitz and SoftBank.

While Flexport's business was thriving during the Covid e-commerce boom, it's been hit hard over the past year as global economic tumult has led to a dramatic slump in global freight movements.

In a series of posts on X, many of which were subsequently deleted, Petersen and his plans for growth at the company. He said Flexport would rescind 55 offer letters, and look to lease out office space.

Prior to the Clark saga, executives had been working on an IPO timeline and were targeting a 2025 debut, according to an internal document viewed by CNBC. Now the company is in cost-cutting mode, and is expected to announce more layoffs in the coming weeks, the people said.

In January, Flexport about 20% of the company's workforce, or roughly 640 employees.

— CNBC's contributed to this report.

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