In 2002, Stoner became the co-host of the Disney Channel's Mike's Super Short Show along with Michael Alan Johnson, an infomercial segment regarding forthcoming Disney releases.
In 2003 and 2005, she appeared as one of the twelve Baker children (Sarah) in the successful comedies Cheaper by the Dozen and Cheaper by the Dozen 2. She has also appeared in several television shows aimed at the preteen market, including The Suite Life of Zack and Cody, That's So Raven and Drake and Josh.
In 2005 Alyson recorded a cover version of the song "Baby It's You" by JoJo. She is currently planning to take vocal lessons in order to focus on transitioning her style from "kiddie-pop" to a richer tone and texture.
She also recently hosted a global fan summit on Amazon.com with good friend and Hannah Montana star Miley Cyrus. Stoner appeared in the Disney Channel Original Movie Camp Rock, along with the Jonas Brothers and then rising star Demi Lovato. In the summer of 2008, she appeared in the Disney Channel Games as a member of the Blue Lightning Team along with Kiely Williams, her Camp Rock castmate Demi Lovato, Shin Koyamada, Roshon Fegan, Cole Sprouse and several overseas Disney Channel actors. She has also appeared as a voice actor in the Kingdom Hearts Video game series.
|2008||Camp Rock||Caitlyn Gellar||Disney Channel Original Movie|
|2010||Camp Rock 2: The Final Jam||Caitlyn Gellar||Disney Channel Original Movie|
|2011||Phineas and Ferb The Movie: Across the 2nd Dimension||Isabella Garcia-Shapiro, Isabella 2||Disney Channel Original Movie, voice|
|2002-2006||Mike's Super Short Show||Sally||Co-Lead role (25 episodes)|
|2004-2006||Lilo & Stitch: The Series||Victoria (voice)||recurring role|
|2005||The Suite Life of Zack and Cody||Max||Recurring 2005-2007 (6 episodes)|
|2005||That's So Raven||Allison "Ally" Parker||"Goin' Hollywood"|
|2005-2006||W.I.T.C.H.||Lillian Hale (voice)||8 episodes|
|2007-2015||Phineas and Ferb||Isabella (voice),
Jenny Brown (voice)
|Main role (Isabella Garcia-Shapiro) and semi-recurring role (Jenny)|
|2013–present||Sofia the First||Princess Mae (voice)||Recurring role|
|2008||Kingdom Hearts Re:Chain of Memories||Kairi|
|2009||Kingdom Hearts 358/2 Days||Xion, Kairi|
|Phineas and Ferb||Isabella|
|2011||Phineas and Ferb: Across the 2nd Dimension||Isabella, 2nd Dimension Isabella, and Receptionist (cameo)|
|2013||Kingdom Hearts HD 1.5 ReMIX||Xion|