After signing with Roadrunner, Pestilence released their debut album, Malleus Maleficarum, in 1988, further refining their approach to thrash metal.

[4][5][6][7][8] By the time they began working on their third album, the lineup changed once again; vocalist and bassist Martin van Drunen departed to front Asphyx.

For their third album Testimony of the Ancients (1991), they enlisted bassist Tony Choy from death metal band Cynic while Patrick Mameli took over the vocal duties.

In 2006, Metal War Productions, working with Martin van Drunen, released Chronicles of the Scourge, containing two concert recordings and one unreleased bonus track.

After a long period of inactivity the band returned in January 2008, The reunion line-up consisted of Mameli on vocals and guitar, Tony Choy on bass and Peter Wildoer on drums.

Speaking to Blabbermouth.net regarding his decision to resurrect the band, Mameli had this to say: It's not a reunion, because I will not be playing with any of the old lineup guys, except Tony Choy, of course so...

[10]In 2008, Pestilence decided to write and record new music for an early 2009 release working with Danish producer Jacob Hansen.

[11] In October 2009, Jeroen Paul Thesseling re-joined Pestilence after fifteen years of separation from the band, replacing Tony Choy's bass position.

[13] On 8 July 2014, vocalist/guitarist Patrick Mameli announced that Pestilence was on a "permanent hold", as he wanted to "concentrate fully" on his new project Neuromorph.

[15][16][citation needed] On 22 February 2017, the band announced via their Facebook page that a new album, titled Hadeon, was due to be released in 2017.

[18] On 24 July 2018, shortly before the bands North America tour was to begin, the metal website MetalSucks reported on a 2017 Facebook post that they alleged showed Patrick Mameli on his personal Facebook profile, in response to a photo of him with blonde dreadlocks, responding to a comment that compared his look to Milli Vanilli with the statement in his native Dutch, "Je zegt dat ik een neger ben?"

Along with the comment, MetalSucks also alleged that the singer also "propagates Jewish stereotypes", pointing to his support of United States President Donald Trump moving the nations embassy in Israel.

[23] On 1 August 2019, Pestilence announced that they had signed to Agonia Records and would release their then-upcoming ninth studio album Exitivm in the coming months.

[24] Several months later, Pestilence announced that Septimiu Hărşan had to leave the band due to restrictions caused by the COVID-19 pandemic; he was replaced by Michiel van der Plicht (God Dethroned and Carach Angren).

[27] In March 2022, Pestilence announced on their Facebook page that they had finished eight songs for their upcoming tenth studio album Portals, with four more tracks to be completed.

[28] In July 2023, it was announced that Pestilence had replaced Joost van der Graaf with Roel Käller as their bassist, and were planning to release their new album later in the year or in 2024.