[4] After his first departure from Testament, Skolnick went on to pursue various musical careers, including briefly replacing Criss Oliva in Savatage for their album Handful of Rain (1994) and a short tour,[5] and starting his jazz band The Alex Skolnick Trio in the early 2000s, which remains active as of 2025.

Skolnick joined the San Francisco Bay Area thrash metal band Testament, then-called Legacy, in 1984 as the replacement of original guitarist Derrick Ramirez.

[10][11][12] Skolnick returned briefly to Testament by re-recording old material for their ninth album First Strike Still Deadly, as well as the Thrash of the Titans performance in 2001.

During the mid to late 1990s, Skolnick led several projects in the San Francisco Bay Area, including Skol-Patrol, a funk band featuring Michael Manring that played themes from police shows.

Since 2002, he has toured and recorded as the Alex Skolnick Trio, a jazz group known for rousing bebop renditions of classic rock and heavy metal tunes.

[16] He said that he intended to have, "musicians from all over the world, driven by acoustic guitar and bringing together inspirational melodies, in-depth improvisation and the passion of the musical styles of Gypsy, Middle Eastern, Indian, Latin, East Asian, Mediterranean, Balkan/Eastern European, African and other indigenous lands – Planetary Coalition has been guided by a single hope: that by weaving the threads that connect musical expressions with regional identities, we can bridge the gap between diverse cultures and people, and increase awareness of the ecological and social issues facing the planet, our island in the sky.

"[17] Planetary Coalition was released by ArtistShare on November 11, 2014 to commemorate the centennial of the end of the First World War.

The project endeavored to combine artistic, ecological, political, and social issues, as well as showcase the landscape and architecture of other countries.

The tune from Mali and from China were first-time guitar-kora and guitar-pipa duos of traditional songs from those regions.

In 2012, he performed live at the Feature Inc Gallery in New York, for a musical interpretation project for the works of visual artist Douglas Melini.

[27] Skolnick plays electric ESP Guitars and Godin hollow-bodied models with Seymour Duncan pickups.

Throughout his days with Savatage he used the RV470 Radius model and an LA Custom Shop prototype based on the Ghostrider series.

[29] Skolnick's influences include Frank Zappa,[1]Eddie Van Halen, Jeff Beck, Jimi Hendrix, Eric Clapton, Johnny Winter, Randy Rhoads, Michael Schenker, Yngwie Malmsteen, Kiss, and Scorpions.