Yes debuted at number four on the UK Albums Chart on sales of 27,639 copies, the duo's highest-placing album since Bilingual (1996). Early sales figures predicted that the album would enter at number one, but its release was beset by distribution problems and Yes proved unable to hold onto its midweek position. The download version erroneously went on sale through iTunes three days before its official release date, rendering 2,500 sales ineligible for the chart, while, the following week, a number of suppliers of the physical album reported stock level problems. The album was hit by a minor manufacturing error as well: some booklets included with initial copies of the Yes etc. double CD set were stapled in the wrong order. EMI set up a website for anyone affected by this to claim a new booklet.
The album was released in multiple formats, including a digital version that included a 48-minute track-by-track commentary on the album, and an 11-disc vinyl version limited to 300 copies, with each disc containing a different album track on the first side and a corresponding instrumental version on the second. The double CD edition of the album incorporated a bonus disc titled Etc., which featured mostly instrumental dub mixes of six album tracks, as well as a new song called "This Used to Be the Future", to which Philip Oakey of The Human League contributed some vocals. A standard, single-disc vinyl LP was also issued, but did not coincide with the international CD and download release.
Yes spawned three further singles. On 1 June 2009, "Did You See Me Coming?" was released worldwide on a number of physical and digital formats, backed with three new B-sides. A limited German-only "Beautiful People" CD and download followed in October. The five-track Christmas, Pet Shop Boys' first EP release (listed under "Singles" on their official website), was released on 14 December 2009, with "All Over the World" acting as the principal radio promo and gaining a music video.
Yes was supported by a comprehensive world tour that stretched across 2009–2012. A recording of the tour made in London in December 2009 was released in a CD/DVD package on 15 February 2010 as Pandemonium.
The album sleeve was designed by Mark Farrow and Pet Shop Boys. The tick on the cover is made up of eleven coloured squares. It was inspired by German artist Gerhard Richter (who is referenced in the album's opening track, "Love etc."), specifically his 4900 exhibition at the Serpentine Gallery and the stained glass window in Cologne Cathedral.
The album's cover was nominated in the 2010 Brit Insurance Design Awards shortlist in the Graphics category.