In 1899, as a ploy to get himself expelled, the student Matthew Fairchild had his friend Christopher Lightwood make explosives and used it to blow up the south wing of the Academy. It was eventually rebuilt.
After being open for centuries, the Academy was closed at some point in the 1990s for unknown reasons. After its closure, Shadowhunter families had gotten used to training their children themselves, either in their homes in Alicante, Idris, or in Institutes around the world.
For the reopening, Vivianne Penhallow was appointed dean. Vivianne found the weeks allotted for the renovation of the school insufficient. Almost all of the teachers left abruptly, their food supply was entirely lacking, and the school was not physically repaired both inside and out, resulting in a troubling reopening. Thus, Vivianne, desperate for any substitutes, asked the warlock Catarina Loss to step in as teacher Academy subjects, particularly History. Delaney Scarsbury was also hired as the training master, and several Shadowhunters were invited to act as guest speakers and lecturers.
While the building itself remained in poor condition, the opening still proceeded as planned and accommodated the first batch of around two hundred new students—including both Shadowhunters and the mundane recruits and Ascension applicants.
Shadowhunters sent to the Academy usually attend only for further training at the age of twelve, after being tutored in Shadowhunter basics at their home until that point. Some young Shadowhunters, however, do not or never did attend the school because their guardians simply chose not to send them, or they weren't accepted because of certain reasons, such lack of previous knowledge of Shadowhunting basics or poor physical condition. An exception to the age rule is also in some situations, as is the case with the much older students, both mundane recruits and the older Shadowhunters, being trained at the Academy after its recent reopening.
There are two 'streams' at the Academy: one for the students who were born Shadowhunters (joined in some cases by experienced or special mundanes) and another for mundanes (called dregs by some of the students and staff). The curriculum for the Shadowhunters is more advanced, with classes for reinforcing their already existing skills in fighting, speaking languages such as the demonic Chthonian, and Marking themselves up with runes. The mundanes, having much more to learn to catch up to the Shadowhunters, studied rudimentary martial arts, basic Shadowhunter history lessons, and memorized the finer points of the Nephilim Covenant—things most of their Shadowhunter classmates already know by then. The two tracks spent most of the day in separate classes, but they began every day together at the training field for an hour of calisthenics.
- The school is the main setting of Tales from the Shadowhunter Academy and is set to be a setting in The Secret Treasons.