Only a week before rehearsals, drummer Joey Kramer was suffering from depression, having grieved the loss of his father a few years prior. With Kramer unavailable, rumors began to circulate that the band would disband. Steve Ferrone was brought in to play drums until Kramer was able to return. "I came back with a nice perspective on what I bring to the table in Aerosmith," Kramer reflected. "That was healthy for me. We ended up rerecording because people were listening to the tracks and were saying some negative stuff about it and saying the band didn't sound the same."
Originally set for a summer release in 1996, the album was delayed, because Columbia Records felt dissatisfied with the nine tracks that Aerosmith and Ballard had produced. Further issues occurred in July that year, when the band asked their manager Tim Collins to step down after almost twelve years of partnership. In his 2014 autobiography Rocks: My Life In and Out of Aerosmith, Perry recounted that Aerosmith felt betrayed by Collins, as he would pit the members against one another. With their longtime manager gone, the band decided to hire in-house producer Kevin Shirley, and set up at Avatar Studios in New York City. Shirley, who had also worked with Journey, helped with the album's overtones and instruments, particularly the guitar sounds. In a 1997 MTV special promoting the making of Nine Lives, Tyler declared: "He's got it somewhere stuck between Toys in the Attic and Rocks."
The new sessions began in September 1996, and continued to November. Following the shift in production, Kramer recovered from his depression, and returned to the studio. Instead of playing his tracks over Ferrone's, the band rerecorded from scratch on all of the completed tracks with Kramer.John Kalodner, Columbia's A&R executive was brought back to supervise the project, after he had been pushed off the production in Florida by Collins. He helped trim the twenty-four songs that had been written to thirteen. Initially, the band called the album "Vindaloo" after adding in elements of Indian music throughout some of the songs, including a sarangi intro by Ramesh Mishra on the song, "Taste of India". But upon completing the track "Nine Lives", the band felt that would make the perfect title, serving as a metaphor for the album's troubled conception.
The booklet for Nine Lives contains 12 pieces of album art (including the cover). Each picture contains a smaller version of the previous picture within itself. The final picture is included in the first, creating an infinite loop. It was designed by Stefan Sagmeister.
The original cover art, inspired by a painting in a book by A. C. Bhaktivedanta Swami Prabhupada, featured Lord Krishna (with a cat's head and female breasts) dancing on the head of the snake demon, Kāliyā. The Hindu community protested, feeling the artwork was offensive. The band had been unaware of the source of the artwork, and the record company apologized, leading to the next prints removing the art from the cover and booklet. The new cover featured a cat tied to a circus knife-thrower’s wheel.
In his AllMusic review, Stephen Thomas Erlewine compared Nine Lives to previous Aerosmith albums stating, “Nine Lives, in contrast, is overlabored, with Aerosmith making a conscious effort to sound hip and vibrant, which ironically simply makes them sound tired." He also criticized the album's troubled production saying, "Not only are the performances perfunctory, but the songs aren't catchy no matter how hard it tries, 'Falling in Love (Is Hard on the Knees)' never develops a hook, and it is not an exception". Elysa Gardner from Rolling Stone was more favorable in her 1997 review concluding, "For those who simply can't abide a collection of Aerosmith tunes without its share of power ballads, Nine Lives doesn't disappoint".
Some releases of Nine Lives feature different track listings, most notably the two Japanese editions which both feature the song "Fall Together". The song was included as a B-side on the album's first single "Falling in Love (Is Hard on the Knees)". The European re-release of the album's third single "Pink", features the B-side "What Kind of Love Are You On". The song was originally titled "What Kind of Lover You Want", and was one of many outtakes left from the recording sessions in Florida. The song was re-titled "What Kind of Love Are You On" and featured in the 1998 movie Armageddon, as well as its associated soundtrack. Another outttake titled "When the Monkeys Come" was reworked by the band in 2000 to promote the release of Charlie's Angels. The song's original title was changed to "Angel's Eye", with some of the lyrics being rewritten to suit the movie's style. Other unfinished tracks that were discarded during the recording sessions in Florida include, "Bacon Biscuit Blues", "Bridges Are Burning", "Heart of Passion", "Loretta" and "Trouble". Tyler also mentioned a song called "Where the Sun Never Shines" during an MTV interview shortly after the album's release.