The Wintersburg Japanese Mission was founded in 1904 as a multi-faith effort, with Episcopalian, Methodist, Presbyterian, Buddhist, and Christian supporters meeting in borrowed barns and cottages. By 1910, congregants had built a mission building and manse, funded by donations from both Japanese American and European American pioneers documented in original ledgers. The church became known as the oldest Japanese church in Southern California. Furuta returned to Japan in 1912 to marry Yukiko Yajima, then contracted with a builder to construct a four-room bungalow. The house was finished by March 1913, months before California's Alien Land Law took effect in May. The law prohibited those ineligible for citizenship from owning property. Because Furuta had purchased and built before the deadline, he became one of the rare Japanese immigrant landowners in the state. By 1917, goldfish ponds covered most of his farm, filled with common and exotic species. Two other families established goldfish farms nearby.

On December 7, 1941, Japan attacked Pearl Harbor. The FBI came to Wintersburg to interrogate Charles Furuta in the sunroom of his bungalow and Reverend Sohei Kowta in the church offices. Furuta was taken first to Tuna Canyon Detention Station in Los Angeles County, then to an enemy alien camp in Lordsburg, New Mexico. He was 61 years old and had lived in the United States for 42 years. On February 19, 1942, Executive Order 9066 established a military exclusion zone. By May, all Japanese Americans had been removed from Orange County. In Huntington Beach, most gathered at the Pacific Electric Railway station near the pier before being bused to the Colorado River Relocation Center at Poston, Arizona. Yukiko Furuta and the children were confined for a year before Charles was allowed to join them. They spent three years at Poston. When they returned to Wintersburg Village in 1945, the goldfish ponds had silted in and the farmland lay in disrepair.

The Furutas spent years recovering their ponds and pivoting their business. Instead of goldfish, they grew water lilies. The farm became the largest provider of cut water lily flowers in the United States during the second half of the 20th century. The church congregation followed their community into confinement and back, with clergy providing shelter and guidance upon return. Reverend Kowta was sent to Little Tokyo to help establish the Evergreen Hostel, a resettlement center for Japanese Americans returning from the camps. The mission supported four Japanese Language Schools across Orange County. The sole surviving school building now serves as the cultural center at Crystal Cove State Park. In 2014, the Presbyterian Church's Presbytery of Los Ranchos issued a formal apology for taking a hands-off position during the incarceration, allowing the present-day Wintersburg Church to separate and return to its non-denominational roots.

The Furuta family sold the property in 2004 after nearly a century of ownership. The buyer, Rainbow Environmental Services, proposed rezoning to commercial and industrial use with demolition of all historic structures. In 2014, the National Trust for Historic Preservation named Historic Wintersburg one of America's 11 Most Endangered Historic Places. The following year, the Trust designated it a National Treasure, one of fewer than sixty in the country and one of only two representing Japanese American history. The site includes the 1910 Mission, 1910 Manse, 1934 Depression-era church, 1912 Furuta bungalow, Furuta barn, and 1947 post-war ranch house. On February 25, 2022, a fire of unknown origin destroyed the manse and damaged the mission building. The remains were bulldozed before investigation could take place. Republic Services, the current owner, has stated plans to sell to Public Storage for self-storage development. The preservation fight continues.