The Society benefited from capable and stable leadership. Belle Bryan served as president until her death in September 1910. Longtime corresponding secretary, Lizzie Cary Daniel succeeded Bryan as president in 1910. Sally Archer Anderson, daughter of Confederate staff officer Archer Anderson and granddaughter of Gen. Joseph Reid Anderson, the man who made Richmond’s Tredegar Iron Works, succeeded her in 1912.

Along with the customary officers, the Museum had a separate hierarchy of regents and vice-regents who oversaw the building and maintenance of the Museum collections. Although the Museum was a local institution, its founders conceived of it as belonging to the whole South. The Museum was separated into rooms dedicated to the collections amassed by each of the eleven Confederate states, and by Missouri and Kentucky (which were represented in both the U.S. and Confederate Congresses) and Maryland (which remained in the Union but provided thousands of soldiers to the Confederacy). Each room had a vice-regent representative, who lived in Richmond and had some connection to the state they served. Then to promote the Museum outside of Richmond, the Society also elected a regent for each room. The regent was a prominent woman living in the appropriate state who, by active work or influence of prestige, attracted contributions of money and relics to the Museum.

The new Museum’s first appeal for donations went out on January 1892. The language reveals the sentimental and commemorative ideas with which the Museum was founded:

"The clothes, the arms, the money, the belongings of the Confederate soldier, and the women whose loyal enthusiasm kept him in the field, are properly objects of historical interest. The glory, the hardships, the heroism of the war were a noble heritage for our children. To keep green such memories and to commemorate such virtues, it is our purpose to gather together and preserve in the Executive Mansion of the Confederacy the sacred relics of those glorious days. We appeal to our sisters throughout the South to help us secure these invaluable mementoes before it’s too late."

The confidence that Southerners would donate artifacts to the Museum proved to be well founded. At first, the items trickled in, but soon began to pour in, although it was four years before the Museum was ready to preserve and display them. The women of the Society built the Museum's collections almost solely on donations that have continued in a steady stream to this day, purchasing only a few items including artwork and furniture. Determined to create a museum that would outlive them, Isabel Maury, Belle Bryan and other Museum founders implemented policies to ensure both the institution’s and the burgeoning collection’s survival. In 1898, at the suggestion of Belle Bryan, the Museum began an endowment fund, which turned into the general fund in the 1930s.