As stated in the book Sainte-Anne: collège et université 1890-1990 the two major events of the decade were the very destructive fires. The rectory burned in 1893 and six years later, the entire College was engulfed in flames.
The priests and the auxiliary of the College who lived in the presbytery were lodged in the juvenate after the 1893 fire.

The fire which started in the kitchen in the early morning of January 16th, 1899, was a disastrous incident for the new college. Within ten days, despite the unexpected tragic event, Father Blanche expressed his desire to rebuild a new college and with the approval of the Acadian population, reconstruction began in the same month. The Acadians of the region supplied all the wood required and Léo Melanson was named responsible for the project. The people of the region spent the whole summer trying to complete the construction so that the college would be ready for the new academic year.

The first College built and destroyed by firei n 1899	The ruins of Collège Sainte-Anne in 1899

Although the College wasn't quite complete, classes began under a new Superior, Father Pierre-Marie Dagnaud, on September 2, 1899.