The mosque has been part of the community for more than two decades. The plan to convert eight separate buildings into one unit began in 2008.
The planning commission approved the plans, but they were halted by the city council.
"We feel that the city's actions were discriminatory. Unfortunately, the level of anti-Muslim, Islamophobia ... around the country is pretty heightened, and we fear that there could have been a few players who took advantage of that bias for their own political gain," said Ameena Qazi of the Council on American-Islamic Relations.
It's against Islamic practice to be crowded together during prayer, and it's also a tenet to be clean for prayer. But leaders say women have to walk all the way across the property after washing and that some are forced into an overflow tent with a TV monitor because the conditions are so crowded.
"We have an adequate space here for what we need to do, but the building itself is very inadequate," said Amy Hossain of the Islamic Center of the South Bay.
City attorney Christi Hogin says it's not about prejudice or freedom of worship, but an issue of zoning and the planning process.
"I acknowledge that they're feeling frustration. The frustration that they're feeling is not from religious discrimination. The frustration they're feeling is the frustration that developers have when they come up against ... local neighborhoods that are resistant to change and planning rules," Hogin said.
The Islamic Center has filed a lawsuit against the city, claiming a violation of their members' freedom of speech, religion and assembly.
"We're looking forward to a solution to this. The solution's going to be in bricks and mortar, it's not something that a courtroom is going to need to decide," Hogin said.
Part of the opposition to the plan involves parking in the neighborhood. But leaders of the mosque say the new plans will accommodate more parking and relieve that congestion on Fridays.