The perpetrators scrawled anti-Christian slogans on the side of the Baptist House, including: "Death to Christianity", "Jesus was a son of a whore", and "We will crucify you".
Three cars parked at the compound had their tires slashed.
The graffiti also included the phrase "price tag", leading police to suspect the involvement of radical right-wing elements that have taken to striking out at churches and mosques in response to the Israeli government's uprooting of Jewish communities in compliance with Arab demands.
"Officers are investigating a strong possibility of a nationalist motive, but no one has been apprehended yet," said police spokesman Micky Rosenfeld.
Israel's mainstream nationalist camp has repeatedly denounced the actions of the apparently de-centralized "price tag" gangs.
But the Baptist House has been a target since long before the start of the "price tag" movement. Situated near some of Jerusalem's most Orthodox neighborhoods, the Baptist House has suffered numerous acts of petty vandalism, and the main sanctuary was set ablaze in 2007.
Looking at the broader picture, some have suggested that the general increase in hostility toward Christians and Messianic Jews in recent years is actually a good sign. As the message of the Gospel reaches more Israelis, increased resistance should be expected.
Photos of the latest vandalism:
From right to left: 'Jesus was a son of a whore'...'price tag'
'we will crucify you'
From right to left: 'price tag'...'we will crucify you'
'death to christianity'