On March 14, 2006, President George W. Bush visited Canandaigua Academy to inform the public about the Medicare prescription drug benefit, also called Medicare Part D. In 2007, renovations were made on the southwestern wing of the building.

Additionally, an expansive field house was appended to the gym on the southern side of the building to meet the needs of the Physical Education department.

On May 5, 2009, a student named Tom Kane killed himself with a shotgun in a bathroom stall at Canandaigua Academy.

In 2018 the Canandaigua Academy Cheerleaders won the NYSPHSAA Division 1 (Small) Championship, coached by Laura Burgess, Candace Foley, Kirstyn Morrell, and Maria Catalano.

The choral department was formerly led by nationally recognized music educator Amy Story.

Retiring in 2015, Story was honored as the American Choral Directors' Association's "Helen Kemp Award" winner in 2012 for a lifetime commitment to vocal and educational excellence.

[7] She is a registered NYSSMA adjudicator, an active member of ACDA, a conductor for numerous honor choirs across New York and Pennsylvania, and continues to work with the Rochester Philharmonic Orchestra (RPO).

Since 2006, the Canandaigua Music Department has hosted a number of guest musicians and artist/educator visits including: The Canandaigua Academy Players, led by Megan Davis, Luc Pereira , and Jim Kelly, has also been recognized for its achievements by Channel 10 News 2017 Rochester ROCS Best Theatre Company and Rochester Broadway Theater League's "Stars of Tomorrow," having taken high honors for many of its musicals.