Chased by paparazzi on motorcycles and TV cameras in helicopters, the car brought Lohan, 24, from the Beverly Hills courthouse, where she had surrendered, to the covered parking garage of Century Regional Detention Facility in Lynwood, Calif.
The actress was booked into custody at 10:11 a.m. and underwent routine medical and psychiatric tests.
"She's been extremely cooperative," says Steve Whitmore, spokesman for the Los Angeles County Sheriff's Department, which operates the jail. "She's going to be a keep-away, meaning she'll be kept away from the general population."
The jail – the same place where the actress, 24, previously served 84 minutes – was "on lockdown," a jail trusty tells PEOPLE.
"Everyone has been kicked out of bathrooms, lobby, everything. For two hours," says Nancy Lozano, who is in the jail's work release program.
Sirens went off around 9:30 a.m. Tuesday and inmates were sent back to their cells, adds Lozano. "The only people who can walk through common areas are deputies," she says.
Though Lohan received a 90-day jail sentence, legal experts say she'll likely only serve between two weeks to a month due to the Sheriff's Department's long-standing policy of releasing nonviolent offenders early due to overcrowding.
Additional reporting by KEN LEE