In the 90s, she took on working in different films, collaborating with other music directors, such as Anu Malik, Anand-Milind, Rajesh Roshan and Nadeem-Shravan. Throughout these years, she had several Bollywood hit songs, including Tere Ishq Mein Nachenge (Raja Hindustani), Chaa Raha Hain Pyaar Ka Nasha (Chandramukhi)), Roundhe (Pyar Tune Kya Kiya), Sona Sona Roop Hai (Bollywood/Hollywood), Mouje Mein (Karobaar), De Diya (Keemat), Ruk Ruk Ruk (Vijaypath) and the controversial Sexy sexy sexy Mujhe Log Bole (Khud-daar).
Simultaneously with playback singing, she has recorded many songs as a pop singer, with album releases. Chinai was noted for her 1995 hit single and album, titled Made in India, which was composed by Biddu. Made in India went on to become one of the highest selling pop albums of its times and Alisha became a household name. This album also contains another well-known songs like, "Aaja Mere Dil Mein", "Ek Baar Do Baar", "Sun O Meri Dhadkan", "Tu Kahan", "Ooh La La", "Tu Jo Mila", "Dhokha Diya Hai Re Tune Mere Dil" and "Lover Girl". With the success of this album, Alisha announced her departure from playback singing and wanted to concentrate only on private pop albums. However, her follow-up albums were less successful. This was also the period when she got into a major controversy with the man who recorded several hit songs with her, Anu Malik. During the release of Made in India, Alisha had accused Anu Malik of molesting her. While some claim it was a publicity stunt by the singer to promote her album, Anu Malik and Alisha did not work for several years, only to reunite in 2003 with Ishq Vishq.
In 2005, she had one of her highest career points came with the song Kajra Re (Bunty Aur Babli). The song was a hit and Alisha won her first and only Filmfare Award for Best Female Playback Singer.