In the late 1930s, the famous bell tower, and headmaster's office, were destroyed to make room for a second extension.

[1] In 2005, the Education and Recreation department of Aberdeenshire Council began investigating the consolidation of the school at a single site.

In September 2009, the Scottish Government announced that the academy would be one of fourteen secondary schools in Scotland to be rebuilt as part of a £1.25 billion programme.

[2] In 2015, the school was relocated to the new purpose-built Ellon Academy Community Campus on Kelly Pearl Way to the south of the town.

[7] Ellon Academy was made a case point during a First Minister's Questions, where it was criticized for its split campus layout and general disrepair.