Home health aide Randi Creighton from Southwest Philadelphia noticed the difference as she passed through the 69th Street Transportation Center.
"We loaded on the back. Social distancing has been great," Creighton told Action News.
At least 16 SEPTA employees have tested positive for the virus.
"We're doing everything we can to just make sure that everybody's safe, that our vehicles are clean as they need to be and sanitary," SEPTA General Manager Leslie Richards said.
Richards explained that the transit agency is continually looking for more ways to increase safety.
Starting Wednesday, riders are boarding buses and trolleys in the back, with on board payment suspended.
Riders with disabilities can still board through the front.
"Only come out if you have essential trips. We are here if you need us, but if you don't need us, please stay home," Richards emphasized.
SEPTA is also limiting the number of passengers on board to further promote social distancing.
Creighton appreciates the effort, but worries how it will affect scheduling.
"With people having work at certain times and the bus schedules being the way they are, I think they may need to add more buses, accommodate getting to work on time," said Creighton.
Richards explained, "Today is the first day- we are closely monitoring, and we will adjust, and where more buses are needed, we will go back and consider and see if we can make that adjustment."
Other measures have already been put into place, including additional cleaning and only using buses with protective shields.
SEPTA is currently installing similar protective shields on trolleys and the Norristown High Speed Line.
The transit union had voiced concerns in recent days about the safety of drivers and operators.
Riders are still taking their own precautions, like Nancy Ferguson of Havertown.
"I take my own precautions because you can't expect them to do everything," Ferguson pointed out.
RELATED: Social distancing: What is it, and how it slows spread of coronavirus