The congregation has survived the destruction caused by fires and floods throughout its history. In November 1852, fire destroyed its original location at 7th and L streets, and it met in congregants' homes until 1858. A Methodist congregation had constructed a building on their former lot during this time, and in 1858 B'nai Israel purchased this new building. Three years later, it too was destroyed by fire. In 1864, the congregation purchased a former Presbyterian concert hall on 6th street for use as their synagogue. In 1904, the congregation moved to 1421 Fifteenth Street, which also caught fire in 1912, and reopened after a year of renovations. This location was home to B'nai Israel until 1954, when the congregation moved to its current location at 3600 Riverside Boulevard. Through the next few decades, the campus expanded to include the Harry M. Tonkin Memorial Chapel, the Sosnick Library, and the Buddy Kandel education wing.
Roots of other synagogues
Between 1858 and 1861, a splinter group, calling itself B'nai Ha'Shalom had formed due to differences of opinion. The groups reunited in 1861 following floods that damaged the Bet Shalom cemetery. In 1879, the congregation turned from Orthodoxy to Reform, affiliating with the Union of American Hebrew Congregations in 1885. The more Orthodox members left to form Sacramento's Mosaic Law Synagogue. In 1970, members left the congregation to form Temple Beth Shalom in protest to the firing of the congregation's cantor.
On June 18, 1999, B'nai Israel was one of three Sacramento synagogues that were set ablaze by white supremacist brothers Matthew and Tyler Williams. The attacks caused more than one million dollars in damage, with B'nai Israel alone sustaining over $800,000 in damage to its sanctuary and its library, which was destroyed. Undeterred, the congregation met at the Sacramento community center that same evening for Shabbat services, and days later held a rally that drew over 5,000 people from the larger community. The arsonists subsequently murdered a gay couple, Gary Matson and Winfield Mowder, in Redding, California. The attack was the second time that the congregation had been the target of a hate crime: the synagogue was firebombed by a 17-year-old white supremacist in 1993.