By Paul J. Davies

The chief executive of fintech giant Wirecard AG resigned Friday after two banks in the Philippines meant to be holding over $2 billion on behalf of the company 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 marked a turning point in the scandal engulfing the company, once one of Europe's rare tech success stories. Shares in Wirecard resumed their free fall, erasing another $2 billion in market value after losing nearly $9 billion on Thursday. The shares are down 75% over two days.

The company scrambled Friday to stanch the damage and keep itself afloat. In a statement, Wirecard said it is in "constructive discussions with its lending banks with regard to the continuation of the credit lines," a reference to EUR2 billion worth of credit lines that can be canceled Friday because the company delayed the announcement of its 2019 financial results.

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 credit-card networks run by Mastercard and Visa. Both companies declined to comment on Wirecard's situation.

Wirecard operates in a highly competitive, but fast-growing and lucrative business, which 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 in a $35 billion buyout by Fidelity National Information Services in 2019.

Wirecard also owns a bank based in Germany, which it uses to partly fund lending to some merchants it services. Merchants often use multiple providers in cases of outage, but they also are sticky customers for payments processors since switching involves technology and hardware costs.

Wirecard's steady rise -- pumping out ever-higher revenue and profits -- also attracted skeptics. Short sellers, investors who bet on a company's share price to fall, repeatedly accused the company 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 the company's shares, according to FactSet, worth -- until two days ago -- around $1 billion. After the stock price collapse of the past two days, those shares were worth around $200 million. Filings show 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. Mr. Marsalek and Mr. Braun had worked together since Wirecard's early days. Mr. Marsalek hasn't responded to requests for comment.

It isn't clear where the missing EUR1.9 billion is or if it ever existed. Critics of the company, including investors who have made bets on its stock price to fall, have said the missing money 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.

Before his resignation Friday, Mr. Braun tried to deflect blame in a company video. He said that 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."

Members of Wirecard's management, including Mr. Braun, are currently under investigation by the Munich prosecutor after German financial regulator BaFin filed a criminal complaint of market manipulation against them. The case was examining whether management withheld information ahead of the April release of a report examining allegations against the company.

The Munich prosecutor didn't immediately respond to a request for comment on Friday.

The auditor, Ernst & Young GmbH, had become suspicious of letters purporting to confirm the existence of the accounts and the amounts held in them, Wirecard said Thursday.

The two Philippine banks confirmed Friday that those letters were fraudulent.

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

In a statement, 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, who was the trustee in charge of the accounts, according to a person familiar with the situation, didn't return calls or emails seeking comment.

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.

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

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