The band's style of music developed with the arrival of John Frusciante (guitar), producer Michael Beinhorn observed, 'It was apparent early on that John was the perfect guitarist for the band - he brought the elements of songwriting and composition to the band which they'd never truly had prior to his involvement. I believe that John is a pivotal figure in the Chili Peppers, being that he is such a distinctive songwriter.'
Frusciante altered the band's sound by introducing melodies, harmonies and more complex song structures. In contrast to the group's previous albums, which featured groove and rhythm-based songs, 'Mother's Milk' contained melodic compositions that reflected the new guitarist's influence. Most of the record, due to Beinhorn's presence, is composed of heavy metal guitar riffs and excessive layering.
'Mother's Milk' features an array of musical styles in its thirteen tracks. Among the songs that surfaced from the Hully Gully sessions in early 1989, 'Knock Me Down' became one of the most radical shifts in style for the band. The introspective lyrics, which analyze the death of Hillel Slovak and the devastating effect drugs can have on life, were a new approach for Kiedis, who primarily wrote of sexual intercourse and a hedonistic lifestyle. The vocalist did not, however, want the track to be associated with 'anti-drug' sentiments, claiming, '[the song] is about letting your friends know that you need help and then being willing to accept the help of others when you need it, whether it's from drugs, or from a number of other personal problems.' According to music journalist Jeff Apter, the song 'Knock Me Down' was 'clearly the most important track the band had ever laid down; it proved that these Peppers were more than knuckleheads.' Musically, the track integrates the Chili Peppers' typical punk influences, but asserts heavier emphasis on melody and harmonics that lead into more alternative territory. 'Knock Me Down' was originally recorded to be a duet between Kiedis and Frusciante, but the song was remixed before being released as a single; the new mix accidentally highlighted the guitarist's voice instead of Kiedis'.
'Higher Ground' became another song that helped the band achieve international success. Originally written and recorded in 1973 by R&B singer Stevie Wonder, the track was, according to Flea, a perfect cover for the band: '...the lyrics are great. Especially as far as the situation that the band has been in, as far as state of mind, for the past few months. That song is really about raising and uplifting yourself spiritually.' The bassist affirmed that the reason the band covered the song was to pay homage to Wonder and the important role he played in popular music. The cover begins with a funk bass-line, followed by multi-layered heavy metal guitar progressions and effects-treated vocals. 'Higher Ground's chorus features backing vocals from an array of friends and engineers who worked on the record; the individuals' competence in singing was irrelevant to the band because they sought to achieve a sense of unity. Mother's Milk was composed of a variety of songs that expanded the Chili Peppers' repertoire. The instrumental 'Pretty Little Ditty' was one of the few songs that featured no guitar layering; Apter notes that the song is 'a dreamy, sweetly stoned instrumental featured deft picking and strumming from Frusciante, intertwined with blasts of trumpet from Flea.' The eclectic track was originally intended to be over three minutes long, but was cut to just under 2 minutes before the album's release. 'Taste the Pain' reflects a more meditative and melodic theme, similar to 'Knock Me Down'. Frusciante introduces psychedelic guitar progressions in the verse, while the lyrics touch on themes of love and loss. Other tracks such as 'Stone Cold Bush' presented topics of prostitution while 'Punk Rock Classic' was, in retrospect, an emulation of typical punk rock songs by Black Flag and The Germs-bands that were influential to the Chili Peppers.