As FIFA’s first and only outside auditor, KPMG has worked for the organization since 1999, one year after Sepp Blatter, who resigned on Tuesday as president just days after being re-elected to a fifth term, began his tenure. KPMG took on a client long criticized for its lack of transparency and its corporate governance issues.

But it is an important relationship for both sides. For FIFA, it means a member of the Big Four accounting club is signing off on its books. KPMG also audits, at FIFA’s request, dozens of FIFA member associations — 40 of them last year. “Having one of the big auditors of course helps to give some credibility to your accounts,” said Jean-Pierre Méan, an advisory council member at Transparency International Switzerland, part of a global anti-corruption organization.

Over its most recent four-year financial cycle, 2011 to 2014, FIFA had $5.7 billion in revenue, mostly from the sales of rights to marketing, licensing, television broadcasting and hospitality, and more than $5.4 billion in expenses. It has reserves of more than $1.5 billion. Referring to its “internal controls system,” or I.C.S., intended to root out fraud, FIFA wrote in its 2009 annual report that “communication with KPMG is extremely important for the members of the internal audit committee because KPMG as external auditors have a very detailed picture of the FIFA I.C.S. following the in-depth audits that they have performed.”

Roger Neininger, the board chairman of KPMG in Switzerland, took the podium last week at FIFA’s annual congress in Zurich, just two days after the United States Justice Department indicted 14 current and former senior FIFA officials and sports marketing executives on 47 counts of racketeering and corruption. Mr. Neininger has been the auditor-in-charge of FIFA’s annual report since 2011, though the 2014 report omits that title. His role at the closed-door sessions, to recommend that FIFA’s executive committee approve KPMG’s signoff on the year’s annual report, sent a clear signal: KPMG was standing by its client.

Accounting firms often contend that their audits are only as good as the information they receive from clients, but they are supposed to recognize patterns or anomalies that suggest they should dig a little deeper.