On 9 April 2016, Pavlidis signed a professional contract until the summer of 2019. On 15 May 2016, he made his debut with the club as a substitute in a 2. Bundesliga 4–2 away win against 1. FC Heidenheim.
Loan to Borussia Dortmund II
On 26 January 2018, Pavlidis joined Borussia Dortmund II on loan for the second half of the season.[4] On 22 June 2018, Pavlidis loan spell was extended until summer 2019.[5]
Loan to Willem II
On 17 January 2019, Willem II confirmed the signing Pavlidis on loan from Bochum until the end of the 2018–19 season.[6] On 23 January 2019, he scored his first goal with the club after Marios Vrousai's assist in a 3–2 away KNVB Beker win against FC Twente.[7] On 16 February 2019, he scored his first goal in Eredivisie.[8]
Willem II
On 29 April 2019, Pavlidis signed a permanent deal with the club.[9] Subsequently that year, on 2 August, in the opening game of the 2019–20 Eredivisie Pavlidis scored twice as Willem II defeated PEC Zwolle 3–1.[10]
AZ Alkmaar
On 9 July 2021, Pavlidis signed a contract until 2025 at Dutch club AZ Alkmaar. Later that year, on 1 December, Pavlidis is one of the eleven nominees for the 2021 Puskás Award.[11]
Benfica
On 1 July 2024, Pavlidis joined Primeira Liga side Benfica on a permanent deal, signing a five-year contract with the club;[12] the transfer reportedly commanded an €18 million fee, plus €2 million in possible add-ons, and a 10% sell-on clause in favor of AZ Alkmaar.[13]