During her time in office, she began rebuilding the Academy (now Saint Mary-of-the-Woods College)[1] and sent Sisters of Providence to staff military hospitals in Indianapolis and Vincennes, Indiana during the American Civil War.

[3]: 268–291 Upon returning, Bailly spent time teaching at the Academy, now Saint Mary-of-the-Woods College, and took full administrative charge of the institute in 1848.

During her administration, she sent Sisters of Providence to staff schools in many Indiana towns including Washington, New Albany, Cannelton, Fort Wayne, Indianapolis, Loogootee, Vincennes and Lafayette.

[5]: 114–121  In the congregation's elections of 1868, Mother Mary Cecilia did not receive dispensation to continue as Superior General and Sister Anastasie Brown was named instead.

For some time, there was talk of creating a new branch of the Sisters of Providence, with Mother Mary Cecilia in charge, on the old Bailly Homestead Porter County, Indiana.

[8] However, with the 1874 election of a new Superior General, Mother Mary Ephrem Glenn, these plans ceased and the community returned to a mostly united group.