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In 1998, parents and teachers, inspired by the Waldorf model of education, founded Monterey Bay Charter School. The original Kindergarten was located in Monterey and 1st-6th grades were located in Marina and subsequently in Seaside with a small but growing enrollment. Until 2005, MBCS was a title program of the San Lorenzo Valley Unified School District and offered a homeschool component.

The school moved in 2001 to its current location, a former Pacific Grove elementary school campus. Although the buildings are quite old and in need of refurbishing, there is a large, grassy playground spilling into a forest of coastal live oaks and Monterey pines. School festivals and assemblies are held in the beautiful outdoor areas of the playgrounds.

In 2006, the school was given its first autonomous charter status by the Board of the Monterey County Office of Education (MCOE). During the school year 2006-2007, MBCS faculty and staff began the rigorous process of creating standards-based benchmark assessments to track student progress. The new charter brought about a significant change in the function and governance of the school. The school's charter with the County eliminated the homeschool component and articulated the school's new responsibilities for accountability with the Office of Education.

In the fall of 2007, the two Kindergarten classes were moved to Seaside as the school grew beyond the available space in Pacific Grove. As part of the school's goal of diversity and accessibility, the school is working to re-locate to the Seaside/Marina area and reunite the Kindergarten with the grades.

The school currently enrolls 425 students and is growing to 500 with three Kindergarten classes and two classes per grade from 1st to 8th. With an API score of 887, the Waldorf-inspired methods have proven successful with stringent State and County testing and accountability standards.

At its annual review of the school, the County Board of Education commended MBCS in successfully providing a charter school alternative to the County's students. In February, 2012, the Board of Education applauded the school on its achievement and approved a new five-year renewal to the school's charter.