Supporting musicians on the album include frequent collaborators Matt Chamberlain on drums, Jon Evans on bass, and Mac Aladdin on guitar.

Alongside the inspiration from beekeeping, female spirituality and the experiences of women in Christianity play a large role, particularly in songs such as "Original Sinsuality" and "Marys of the Sea".

[5] The Beekeeper was recorded throughout 2004 at Martian Engineering Studios in Cornwall, England, with the mixing handled by Amos' husband Mark Hawley and Marcel van Limbeek.

[4] In addition to Chamberlain, Evans, and Aladdin, the London Community Gospel Choir appears on the tracks "Sweet the Sting", "Mother Revolution", "Witness", and "Hoochie Woman".

[7] "Sweet the Sting" is a primary example of the album's soul influence, enhanced by the prominent vocals of the London Community Gospel Choir and Amos' Hammond B-3 organ.

The track was written as a response to frequent use of the word "terrorist" (particularly after the September 11 attacks) and to those who twist the term for their own personal or political gain.

[4] The song took inspiration from the Daphne du Maurier novel of the same name, and stories from Cornwall locals of ships running aground and being looted by wreckers.

As Amos said in a 2005 interview with Uncut: "what I find really disturbing about this global war, is you don't see any of the world leaders sending their children to be butchered.

[11] "Cars and Guitars" features prominent upright bass playing by Evans[4] and was inspired by the concept of a woman reaching an emotional breaking point and driving away to abandon her family.

Amos stated the song "suggests it's not sin you find in the garden, it's original sinsuality", a term created to represent a situation in which her character is encouraged to eat from the tree of the knowledge of good and evil, rather than being dissuaded from it.

"[14] "Martha's Foolish Ginger" is a track which Amos has said to have worked on over a period of several years, having created its title and written its chorus while struggling to finish the song until being inspired by a trip to San Francisco during her 2003 Lottapianos tour.

Inspired in part by a book entitled Sextrology, "Goodbye Pisces" portrays the end of a relationship with lyrics influenced by astrological signs and ages.

[11] Amos wrote the song with the intention of including multiple different sides to the story of Mary Magdalene; both as her being part of the sacred marriage, but also tackling the sexist attitudes towards women held by Saint Peter, Paul the Apostle, and many hailing from early Orthodox Christian tradition.

[11] Amos also cited the tale of Melusine, a figure in European folklore described as having the upper-half of a woman and lower-half of a fish or serpent (similar to a mermaid), as an inspiration for the song.

Barry Walters of Rolling Stone praised the album's second half, highlighting the "harrowing starkness" of "Original Sinsuality" and the title track's electronic elements, but found its length "frustrating" and stated that "with some ruthless editing and remixing, this maddeningly uneven eighty-minute disc could have been her best in ages.

"[23] Subsequently, Amos would apply a band-centric ethos to American Doll Posse (2007) and a heavy emphasis on arrangements for Abnormally Attracted to Sin (2009) in contrast with the approach of The Beekeeper.

Amos was joined by the London Community Gospel Choir during the June 4 show, appearing on "Mother Revolution", "Witness", "Sweet the Sting", and "Hoochie Woman".

[26] The Salt Lake Tribune called the September 6 concert at the USANA Amphitheatre "smoldering" and gave particular praise to the performance of "Winter".