Munich prosecutors confirmed that Braun was arrested on suspicion of having inflated the digital payment company's balance sheet and sales through fake transactions, reports CNN.
He did this in order to make the company more attractive to investors and customers.
Braun was likely to be released from custody on a bail of $5.7 million, according to the prosecutors.
Earlier, Germany-based Wirecard said on Monday that 1.9 billion euros (nearly $2.1 billion) that were supposed to be in its accounts simply did not exist at all.
"The Management Board of Wirecard assesses on the basis of further examination that there is a prevailing likelihood that the bank trust account balances in the amount of 1.9 billion EUR do not exist," the company said in a statement.
Braun resigned last Friday after global market consulting firm EY said the cash, which makes up roughly a quarter of the company's assets, could not be located.
The central bank of Philippines said that none of the money appears to have entered the country's financial system. The central bank is also investigating the case.
The German firm has withdrawn its financial results for 2019 and for the first quarter of 2020.
Founded in 1999, Wirecard was once considered one of the most promising tech firms in Europe. It processes payments for consumers and businesses, and sells data analytics services.
The company has nearly 6,000 employees in 26 countries around the world.