The Madrid regional government claims that the two drivers overcharged ride sharers by asking for more than just a proportional share of petrol and road tolls, regional transport director Pablo Rodriguez Sardinero told AFP.
BlaBlaCar said the drivers deny the charges, which could lead to hefty fines for the drivers and the company, which is present in 22 countries and boasts 35 million members.
The drivers risk fines of €4,001 ($4,400) each, and the company €8,803 for facilitating "an unlicenced transport service".
The Madrid region says that insurance and financing costs for the purchase of vehicles cannot be charged to carpool users.
French-founded BlaBlaCar said the drivers had respected "the platform's norms and therefore the current legislation".
The platform is popular in Spain where it started out in 2010 at the height of the financial crisis. It has around three million users there.
A company source told AFP that BlaBlaCar employs staff specifically to ensure that users cannot make a profit beyond sharing the cost of a ride.