2016 that Pękalski signed for Halmstads BK on a two–year contract. However, he continued to be sidelined for the next three months, due to his continuous injury concern that he sustained last season. It wasn't until on 18 June 2016 when Pękalski made his debut for the club, starting the match and played 69 minutes before being substituted, in a 5–2 loss against IK Frej. Since joining Halmstads BK, he quickly established himself in the first team, playing in the midfield position. Pękalski played in both legs for the league's play–offs against Helsingborgs, as Halmstads won 3–2 on aggregate to send the club promoted to the Allsvenskan next season. Despite missing two matches later in the 2016 season through suspension, he went on to make sixteen appearances in all competitions. At the start of the 2017 season, Pękalski continued to establish himself in the first team, playing in the midfield position. He then captained the side for the first time, coming against IFK Norrköping on 4 March 2017, as the club lost 7–0 in the Svenska Cupen. Pękalski captained three more times for Halmstads BK in the next four months. Despite missing two matches due to suspension up until his departure, he went on to make eighteen appearances in all competitions. Prior to his departure from the club, Halmstads BK have been discussing with the player over a new contract. Oxford United On 8 August 2017, it was confirmed that Pękalski had left Halmstads to sign for EFL League One side Oxford United on a two-year deal for an undisclosed fee. Upon joining the club, he was joined by Manager Pep Clotet, who was his coach during their time at Malmö FF and teammate, Agon Mehmeti. Just four days later, Pękalski suffered a cruciate ligament injury during training which ruled him out until the New Year. By February, he made his return to training and was featured in Oxford United's friendly matches. Despite his return from injury, Pękalski never played for the club for the entirety of the 2017–18 season. Following this, he was told by the club that he can leave Oxford United after being deemed surplus to requirements. Loan to Halmstad On 18 July 2018, Pękalski re-joined Halmstads on loan until November 2018. He made his second debut for the club, coming on as a 64 minute substitute, against Degerfors on 31 July 2018 and set up a