By Paul J. Davies

The chief executive of Wirecard AG resigned after two banks in the Philippines meant to be holding over $2 billion on behalf of the fintech giant said they don't have the cash and never did.

Chief Executive Markus Braun, long the face of the company and its largest shareholder, resigned with immediate effect, the company said Friday. James H. Freis, who was appointed as a member of Wirecard's management board late Thursday, will serve as interim chief executive.

Mr. Braun's abrupt resignation marks a turning point in the scandal engulfing the Munich-based company, once one of Europe's rare tech success stories. Shares in Wirecard resumed their free fall Friday, erasing another $2 billion in market value after losing nearly $9 billion the day before. The shares are down 75% over the two days.

On Thursday, the company said its auditors had become suspicious of letters purporting to confirm the existence of the accounts at the Philippine banks, and on Friday the banks confirmed Friday the letters were fraudulent.

The company scrambled to stanch the damage and keep itself afloat. Wirecard said it was in discussions with its lending banks about the continuation of credit lines. It has EUR2 billion ($2.2 billion) worth of credit lines that can be canceled Friday because it delayed reporting its 2019 financial results.

In a sign of the seriousness of its situation, Wirecard on Friday evening appointed Houlihan Lokey, Inc., an investment bank that specializes in restructurings, to develop a plan "for the sustainable financing strategy of the company together with Wirecard."

Wirecard is one of a set of companies that have boomed as commerce shifted online and away from cash payments. It processes electronic payments for retailers, gambling sites, travel companies and others, especially online, and provides related services and loans.

The company connects merchants with the banking system, including through networks run by Mastercard and Visa. Both credit-card companies declined to comment on Wirecard's situation.

Wirecard operates in a highly competitive, but fast-growing and lucrative business that has seen a wave of mergers in recent years. Rivals include the likes of Square Inc., Netherlands-based Adyen and Worldpay, which was scooped up last year in a $35 billion buyout by Fidelity National Information Services.

Wirecard also owns a bank based in Germany, which it uses to help fund lending to some merchants it services. Merchants often use multiple providers to guard against outages, but they also tend to stick to their payments processors since switching involves technology and hardware costs.

Wirecard's pumped out ever-higher revenue and profits, and its steady rise attracted skeptics. Short sellers, investors who bet that a stock will fall, repeatedly accused Wirecard over several years of fabricating business and cash. The company vociferously denied those allegations -- and its stock kept rising.

Mr. Braun, a 50-year-old computer scientist from Vienna, had been Wirecard's chief executive and chief technology officer since 2002. Tall and known for his intense manner of speaking, he adopted the sartorial style of the tech world, wearing black turtlenecks similar to Apple Inc. founder Steve Jobs.

He controlled around 7% of Wirecard's shares, according to FactSet. Worth roughly $1 billion two days ago, they are now worth about $200 million. Filings show that in the past he had pledged some shares for loans.

"The confidence of the capital market in the company I have been managing for 18 years has been deeply shaken," Mr. Braun said in an emailed statement. "With my decision, I respect the fact that responsibility for all business transactions lies with the CEO."

On Thursday, the company also suspended its long-serving chief operating officer, Jan Marsalek, without giving a reason. Messrs. Marsalek and Braun had worked together since Wirecard's early days. Mr. Marsalek hasn't responded to requests for comment.

It isn't clear where the EUR1.9 billion went missing or if it ever existed. Critics of the company, including short sellers, have said the amount may represent a hole that has been growing for years because revenue reported from third-party affiliates wasn't real. The company has in the past denied those allegations.

In 2018, a company whistleblower in Singapore pointed to backdated contracts and falsified invoices that eventually became the subject of a police investigation in the city state.

Shortly before his resignation Friday, Mr. Braun tried to deflect blame, saying the company could itself be a victim. "At present it cannot be ruled out that Wirecard has become the aggrieved party in a case of fraud of considerable proportions," he said in a company video.

Members of Wirecard's management, including Mr. Braun, are currently under investigation by the Munich prosecutor after German financial regulators filed a criminal complaint of market manipulation against them.

Anne Leiding, a spokeswoman for the Munich prosecutor's office, said prosecutors were continuing to investigate the "entire Wirecard situation, including the latest developments."

The missing EUR1.9 billion is meant to be held in accounts looked after by a trustee on behalf of Wirecard and payment-processing partners in some countries. In October, Wirecard appointed KPMG as an outside auditor to look into allegations about the company's accounting practices. In an April report, KPMG said it had problems obtaining evidence of the balances in question.

Wirecard on Thursday reported that auditor Ernst & Young GmbH had raised serious questions about company bank accounts in the Philippines. On Friday, BDO Unibank Inc. and Bank of the Philippine Islands issued responses.

"The document claiming the existence of a Wirecard account with BDO is a falsified document and carries forged signatures of bank officers," a BDO Unibank spokesperson said. It has reported the matter to the Philippine central bank.

Bank of the Philippine Islands said: "Wirecard is not a client. Their external auditor presented to us a document that claimed that they are a client. We have determined that the document is spurious."

Wirecard didn't respond to a request for comment.

A local lawyer based in Makati City in the Philippines was the trustee in charge of the accounts, according to a person familiar with the situation. The lawyer didn't return calls or emails seeking comment.

--Chong Koh Ping and Mauro Orru contributed to this article.

Write to Paul J. Davies at paul.davies@wsj.com