The congregation was founded in 1986, and the synagogue, completed in 1997, includes a 770-seat sanctuary, preschool, afternoon Hebrew school, senior center, library, and mikveh, serving the Jewish communities of Poway and Rancho Bernardo.

[3][4] The congregation first met in a storefront in the Rancho Bernardo shopping center, and then moved to a one-acre site where it opened a preschool in mobile trailers.

[6] On July 14, 2020, Goldstein pleaded guilty to tax and wire fraud for allegedly misusing at least $6.2 million in contributions and donations to the Chabad of Poway.

The district attorney's office said it would recommend probation rather than a maximum five-year prison sentence, due to Goldstein's cooperation with investigators and his "lifetime of service" to the synagogue and community.

[11] On April 27, 2019, John Earnest, a 19-year-old male from the San Diego suburb of Rancho Peñasquitos, entered the synagogue building during services on the last day of the Jewish Passover holiday and opened fire in the foyer.

[16] The shooter's gun jammed after releasing ten bullets[17] and two congregants, one an off-duty United States Border Patrol officer, chased him out of the building.