"Madrid Central," as it is called, was one of the measures that persuaded the European Commission not to take Spain to court last year over its bad air pollution in the capital and Barcelona, as it did with France, Germany and the United Kingdom.
"Fewer cars, better air" and "The new city hall seriously harms your health" were the messages on banners as protesters walked through the city’s center in 40-degree-Celsius heat.
The capital's new conservative mayor, Jose Luis Martinez-Almeida, made ditching "Madrid Central" a priority during his campaign, saying it had done nothing to ease pollution and only caused a nuisance for locals.
But since he has taken power as part of a coalition with center-right party Ciudadanos, city officials have toned this down, saying the government is merely seeking to reform a system that does not work properly, having mistakingly handed out some fines.
When the system was launched in November, Madrid followed in the steps of other European cities such as London, Stockholm and Milan that have restricted traffic in their centers.
But while in these cases drivers can pay to enter such zones, Madrid went a step further, banning many vehicles from accessing the center altogether and fining them if they did.
These fines will be suspended from July 1 to the end of September as the new city hall team audits the system.
For Beatriz Navarro, 44, a university biochemistry professor who took part in the march, the system is working fine.
"It's a small seed ... among everything that has to be done to slow down climate change," she said.
In a statement, environmental group Ecologistas en Accion said "the levels of pollution from nitrogen dioxide (NO2) registered during May this year were lower than those of 2018 in all the [measuring] stations in the system."
"In 14 of the 24 stations [in Madrid], the value registered in May 2019 was the lowest in the last 10 years."