Bishop of Limburg Franz-Peter Tebartz-van Elst, dubbed the "bling bishop" for his extravagances, was received by the pontiff after a tense week's wait in Rome.
A Vatican statement confirmed the audience but did not offer any further details. The meeting lasted around 20 minutes, newspaper the Welt reported.
Tebartz-van Elst hit the headlines following accusations he took a business-class ticket on a trip to India and squandered money on luxuries.
His private quarters in a brand-new bishop's palace are reported to have cost about €2.9 million and included a 63-square-metre dining room and a €15,000 bathtub.
On Thursday, the Pope met Germany's top Catholic cleric Robert Zollitsch for closed-door talks about the scandal.
Before meeting Tebartz-van Elst, the Pope also gave an audience to Joachim Meisner, Archbishop of Cologne, in a meeting planned months before the controversy surrounding the Limburg bishop arose.
Religious observers have speculated that Pope Francis, who has called for "a poor Church for the poor", may decide to make an example out of Tebartz-van Elst, forcing him to resign.
A decision is not expected to be taken until Zollitsch has filed a report the Vatican has requested on the scandal.
The 53-year-old bishop is under pressure to resign after using church funds to build himself the new diocese headquarters, which also include a museum, conference halls and a chapel.
The ostentatious project in the ancient town of Limburg was approved by his predecessor and was initially valued at €5.5 million, but the final bill ballooned to €31 million.