The work on the new building started immediately. It was to be a combination lodge and school building. Upstairs the Masons met and the lower floor was designated for the school. It was during this time, the political cause for Southern Independence had swept Texas and the Southland. War and lack of materials slowed completion of the building, however, it was operational. The lodge minutes are sketchy but by 11 December 1863, a charter was granted by the Texas Legislature, thereby creating San Saba Masonic College. The institution was open to both male and female students and was a two story-story rock structure.

Problems seemed to plague the lodge and school. Qualified teachers were hard to locate, trustees were difficult to keep and hard currency was scarce. Over time the lodge became responsible for some of the children’s tuition. To make matters worse, most of the able- bodied men had gone off to the war while the frontier borders of Texas receded, encouraging deadly Indian raids. By 1865, the War for Southern Independence was lost and Texas would be subjugated with over 51,000 Yankee troops. The lodge continued to meet regularly but little mention is made about the school until August 1879, when the membership considered donating the college to the Methodist Conference. On 4 September 1879, the Masons voted and the San Saba Masonic College came to an end.

San Saba Lodge No. 225 survived Reconstruction and the loss of its school but it could never survive the San Saba Mob. The rustlers in this part of the country were well organized: there was slack law enforcement, poor courts, and an open frontier due to the subjugation of the Indians. By the early 1880s, these conditions prompted many good men to form a vigilante or regulator "mob." This would not just be any impromptu mob to mete out temporary justice, but a highly efficient, well structured, formal organization. The rustlers were quickly routed and at first there was popular support for the "mob." However, after a time the initial leaders learned what all mob organizations eventually learn – that they could not control what they had created.