What seems to have got the German's ziege were PayPal's rules for extra charges and the presentation of PayPal in the terms of use for Germany.
The regulator is investigating in particular rules that say merchants may not offer their goods and services at a lower price to customers who choose a cheaper payment method than PayPal.
PayPal demands that sellers do not express a preference for other payment methods or make their use more convenient for customers, according to the antitrust watchdog.
Cartel office chief Andreas Mundt said: "These clauses could restrict competition and constitute a violation of the prohibition of abuse," said. "We will now examine what market power PayPal has and to what extent online merchants are dependent on offering PayPal as a payment method."