Coil spent the next period of its existence exploring visual media. In late 1984 they recorded a rendition of the Soft Cell smash "Tainted Love," producing a widely banned, hallucinogenic video clip featuring Mark Almond as the Angel of Death; despite considerable controversy at home, the video ultimately found its way to the archives of the Museum of Modern Art. After spending several years working with filmmaker Derek Jarman on the feature The Angelic Conversation, Coil issued a remixed edition of their soundtrack. Following 1986's Nightmare Culture, a collaboration with Boyd Rice produced as split release with Current 93, Christopherson and Balance invited Stephen Thrower to join the group in a full-time capacity. As a trio, they recorded 1986's Horse Rotorvator, an LP introducing classical, jazz, and Middle Eastern textures into the mix, as well as the EP The Anal Staircase.

In 1987, Coil issued The Unreleased Themes for Hellraiser, a collection of atmospheric gothic instrumentals commissioned for but ultimately cut from the Clive Barker horror film, followed by Gold Is the Metal (With the Broadest Shoulders), a remixed history of the group's first several years of work. Unnatural History, another career overview, effectively ended the first phase of the band's career in 1990; when Coil resurfaced a year later with Love's Secret Domain, their music reflected the strong influence of the acid house culture. Another long layoff brought on by financial difficulties ended in 1995, when the group -- now consisting of Christopherson, Balance, and Dean McCowall -- signed to Nine Inch Nails frontman Trent Reznor's Nothing Records label to release Backwards. Additionally, they recorded the LP Worship the Glitch, issued under the name ELpH, and in 1996 cut A Thousand Lights in a Darkened Room as Black Light District, the first in an ongoing series of Black Light District releases.

Across 1998 and 1999, Coil issued a series of four themed EPs: Spring Equinox, Summer Solstice, Autumn Equinox, and Winter Solstice (later compiled for Moon's Milk [In Four Phases]). After adding Thighpaulsandra to the lineup, they issued Astral Disaster (1999), Musick to Play in the Dark, Vol. 1 (2000), Queens of the Circulating Library (2000), and Black Antlers (2004). On November 13, 2004, Balance fell from the second floor landing of his house and passed away. The final Coil recordings featuring his involvement, including ...And the Ambulance Died in His Arms and The Ape of Naples, were released the following year.