As wildfires threatened Malibu, the Pepperdine students didn’t panic. They had a plan.

The wildfire alert came in the middle of the night as some college students in Southern California were cramming for final exams and others were woken up in their dorms.

But rather than run away from the impending blaze, some 3,000 students at Pepperdine University headed toward two buildings at the heart of the 830-acre campus in coastal Malibu, California, to shelter in place.

The protocol at the Christian university with picturesque views of the Pacific Ocean may seem to defy logic to those accustomed to scenes elsewhere in wildfire-prone California of thousands of residents evacuating fire zones in lengthy caravans of cars.

For years, the university nestled in the foothills of the Santa Monica Mountains has had a special protocol due to its unique terrain and design that calls for students to be brought to a library and campus center where they can get food and water and have their basic needs met, said Michael Friel, a Pepperdine spokesperson.

The school began preparing students and community members on what to do in case of a wildfire during new student orientation at the beginning of the academic year. When the fire broke out the night of Dec. 9, school officials started communicating with students around 11 p.m. and activated the shelter-in-place protocol about two hours later, spreading the word through text messages, email, social media, and by going door to door.

“A lot of our students were woken up by a knock on the door, and we made sure they were aware of the conditions and we were able to get them out of harm’s way,” Mr. Friel said.

The Franklin Fire quickly moved south, jumping over the famous Pacific Coast Highway and stretching to the coast, where large homes line the beach. Thousands of Southern California residents were under evacuation orders and warnings Dec. 10 with more than 8,100 homes and other structures under threat.

County fire officials estimated that more than 3.5 square miles of trees and dry brush had burned amid dangerous conditions fanned by dry, gusty Santa Ana winds that were expected to last until Dec. 11.

The cause of the fire was not immediately known.

Ryan Song, a resident assistant at Pepperdine University, said he noticed the power went out at his dorm late Dec. 9. When he looked out the window, he saw a huge pink glow.

“I thought, ‘This is too bright,’ and it got bigger and bigger,” the 20-year-old junior said. “I immediately went outside and saw that it was a real fire.”

Mr. Song and the other assistants went door to door to get students out. Most were calm and followed instructions, he said; a few who were scared rushed to their cars to get off campus.

Mr. Song said he spent the next few hours racing back and forth in the dark between his dorm and the main campus to ensure no one was left behind.

Pepperdine University officials said the campus was designed in the 1960s with fire safety in mind due to the region’s experience with wildfires. Buildings were clustered together and covered in stucco while roadways were constructed to make it easy for firefighters to get in, said Phil Phillips, the school’s executive vice president.

During the 1990s, campus officials worked with Los Angeles County fire authorities to develop a safety plan, and authorities said the safest option for students would be to remain on campus. The school is diligent about brush clearance and has a plan to reduce smoke in shelter-in-place locations by taping shut doors and using air filters, he said.

The nearby stretch of the Pacific Coast Highway can also become congested during an emergency, Mr. Phillips said, such as during the deadly Woolsey Fire in 2018.

“What you don’t want is to be stuck,” said Mr. Phillips, who has been at the campus for three decades – including as a student – and said he has been through seven fires. “Protecting our students, providing for their safety is a moral obligation for us, so we take it really, really seriously.”

On Dec. 10, heavy smoke from the Franklin Fire, burning northeast of the school, billowed over the campus 29 miles west of Los Angeles, and classes were cancelled and final exams postponed. Firefighters had not contained any part of the blaze as of the afternoon of Dec. 10.

The campus was singed but no injuries were reported, and only one structure possibly was minimally damaged thanks to firefighters’ hard work and collaboration from students, faculty, and others on campus, Mr. Friel said.

Jim Gash, the college’s president, said the campus was no longer threatened by the afternoon of Dec. 10.

“I am grateful that through prayer, preparation, and cooperation, our Pepperdine community safely navigated the challenges encountered over the last 12 hours,” Mr. Gash said in a statement. “Our prayers continue to go out to the Malibu community.”

This story was reported by The Associated Press.