Under Advocaat

Although Zenit reached the quarter-finals of the UEFA Cup in 2006, a mediocre start to the league season led to the summer replacement of coach Vlastimil Petržela. In July 2006, Dick Advocaat^[7] took over as Zenit's manager. Advocaat worked together with his assistant manager, former Netherlands national youth team coach Cor Pot. Zenit won the 2007 Russian Premier League—their best league achievement since winning the USSR Championship in 1984—allowing them to compete in the group stage of the 2008–09 UEFA Champions League.^{[citation needed]}

In 2008, Zenit won the Russian Super Cup and reached the quarter-final of the UEFA Cup for the second time in their history. In the first leg of the quarter-final away game against German side Bayer Leverkusen, the team achieved a 4–1 victory. They qualified for the semi-finals of the competition for the first time in their history, despite a 1–0 home loss to Leverkusen in the second leg, and were drawn to play further German opposition in the semi-final, Bayern Munich, considered the top team remaining.^[8] A battling performance in the first leg of the semi-final earned Zenit a 1–1 draw away against Bayern Munich. In the second leg at home, Zenit won 4–0, defeating Bayern 5–1 on aggregate and going through to the UEFA Cup Final for the first time in club history, where they met Scottish side Rangers at the City of Manchester Stadium in Manchester on 14 May. Zenit won 2–0, with goals from Igor Denisov in the 72nd minute and Konstantin Zyryanov in stoppage time, to lift the club's first-ever UEFA Cup. Andrey Arshavin was named man of the match.^[9]

On 29 August 2008, at the Stade Louis II in Monaco, Zenit then defeated Manchester United 2–1 in the 2008 UEFA Super Cup, becoming the first Russian side to win the trophy. Pavel Pogrebnyak scored the first goal and Danny scored the second, the latter being named man of the match in his debut for Zenit.^[10]

In the 2008–09 Champions League group stage, Zenit was grouped with Real Madrid, Juventus and BATE Borisov in Group H, which by some was marked as the "group of death." Zenit ultimately finished in third place in the group, behind Juventus and Real Madrid, and was thus unable to progress to the knockout phase of the competition. This position, however, was good enough to earn the club a place in the 2008–09 UEFA Cup last 32, where the team faced VfB Stuttgart for a place in the last 16 of the competition. After defeating Stuttgart on away goals, Zenit went on to lose 2–1 over two legs against Italian club Udinese.^{[citation needed]}

Under Spalletti

Luciano Spalletti signed a contract with Zenit in December 2009, with Italian coaches Daniele Baldini, Marco Domenichini and Alberto Bartali also joining the Russian club. The Board of Zenit mandated him to return the Russian Premier League title to Zenit, win the Russian Cup and progress from the group stage of the Champions League in his first year.^{[citation needed]}

Zenit won the Russian Cup on 16 May 2010 after beating Sibir Novosibirsk in the final (previously beating Volga Tver in the quarter-finals and Amkar Perm in the semi-finals). After 16 games in the 2010 Premier League, with 12 wins and four draws, Zenit claimed 40 points, setting a new Russian Premier League record for most points won at that stage of the campaign.^{[citation needed]}

On 25 August 2010, Zenit lost its first game under Spalletti to French side Auxerre and failed to advance to the Champions League group stage, instead participating in the Europa League. On 3 October, Zenit beat Spartak Nalchik to set another Russian Premier League record for most consecutive games going undefeated, with 21 games since the start of the league season. On 27 October, however, Zenit suffered its first defeat of the season at the hands of rival club Spartak Moscow, just seven games short of finishing the championship undefeated. On 14 November, Zenit defeated Rostov and two games prior to the end of the season won the championship title, the first in Spalletti's managerial career.^{[citation needed]}

Zenit progressed through the knockout stage of the 2010–11 Europa League in first place, then beating Swiss side Young Boys in the Round of 16. On 6 March 2011, Zenit won against CSKA Moscow in the Russian Super Cup, the third Russian trophy won under Spalletti. On 17 March, however, Zenit were knocked out of the Europa League, losing to Dutch team Twente 2–3 on aggregate in the quarter-finals.^{[citation needed]}

In the 2011–12 Champions League, Zenit began the group stage drawn into Group G alongside Porto, Shakhtar Donetsk and APOEL. On 6 December 2011, the team finished the group stage in second place and for the first time in club's history qualified for the spring knockout phase of Champions League. In the Round of 16, Zenit were drawn with Portuguese side Benfica, winning the first leg 3–2 at home through two goals from Roman Shirokov and one from Sergei Semak. In the second leg in Lisbon, however, Zenit lost 2–0 and were thus eliminated from the competition.

In April 2012, Zenit won their second-straight Russian Championship after beating Dynamo Moscow.^[11]

Under Villas-Boas

After a series of disappointing results in both the Champions League and the Premier League, Spalletti was fired on 11 March 2014.^[12] A week later, the club announced they had negotiated a two-year deal with André Villas-Boas, who himself had been released a few months prior after a disappointing stint as manager of English side Tottenham Hotspur.^[13] In the 2014–15 Europa League, Zenit were eliminated in the quarter-finals by eventual champions Sevilla. In May 2015, Zenit won the Russian Championship, the first championship title under Villas-Boas and the team's fifth-ever on the eve of its 90th anniversary celebration. Zenit then defeated Lokomotiv Moscow in the 2015 Russian Super Cup 1–1 (4–2 on penalties).^{[citation needed]}

Later in the 2015 calendar year, Villas-Boas said that he would be leaving the club after the 2015–16 season. In the 2015–16 Champions League, Zenit began the competition in the group stage. They were drawn in Group H alongside Valencia, Lyon and Gent. They ended the group stage with their best group stage finish ever, winning five out of six matches and emerging as group winners. They were, however, eliminated from the competition in the Round of 16 by Portuguese side Benfica.^{[citation needed]}

On 24 May 2016 Villas-Boas left the club at the end of the season, with Mircea Lucescu appointed the new manager of Zenit.^[14][15]

Under Lucescu and Mancini

In July 2016 Zenit won the Russian Super Cup after a 0–1 victory over CSKA Moscow.^{[citation needed]}

During the 2016–17 Europa League, Zenit began the group stage drawn into Group D alongside Maccabi Tel Aviv, AZ Alkmaar and Dundalk. On 8 December 2016, the team finished the group stage in first place and qualified for the spring knockout phase of Europa League. In the round of 32, Zenit faced R.S.C. Anderlecht and was eliminated 3–3 on aggregate due to the away goals rule. In the league, Zenit's performances in the spring were disappointing and as such the club finished third and missed out on the Champions League for the second year in a row. Zenit was also eliminated in the round of 16 by FC Anzhi Makhachkala 0–4 on aggregate after an abysmal performance. The first (and last) season of Mircea Lucescu was a complete disappointment despite the expectations.^{[citation needed]}

On 1 June 2017 Zenit appointed Roberto Mancini as the new manager of the team.^[16] On 13 May 2018, Mancini terminated his contract by mutual consent.^[17]

Under Semak

In May 2018, Mancini left to become the head coach of the Italy national football team. Sergey Semak became the new manager of Zenit, receiving a two-year contract.^[18]

In August 2018, during the 1st leg of the 3rd qualification round of the UEFA Europa League, Zenit suffered a 0–4 loss to Dynamo Minsk. During the 2nd leg back on home ground, Zenit made a comeback winning 8–1, scoring 3 goals in the second half and 4 goals in the second half of the extra time, with 2 goals scored in the 120th minute.^[19] Zenit went on to beat Molde FK 4–3 on aggregate in the next round, entering the group stage of 2018-19 UEFA Europa League.^[20]

In March 2020, the league was forced to halt due to the COVID-19 pandemic in Russia.^[21] Zenit secured another title on 5 July 2020 after a victory over FC Krasnodar, with 4 games left to play in the tournament.^[22]

On 2 May 2021, Zenit secured their third title in a row in a 6–1 victory over second-place FC Lokomotiv Moscow.^[23] Zenit opened the 2021–22 season with a seventh win in the Russian Super Cup after a 3–0 win over Lokomotiv Moscow, but without major key players who left the club like Yuri Zhirkov, Andrei Lunev, and Sebastián Driussi.^{[citation needed]}

After the 2022 Russian invasion of Ukraine, former Ukrainian international Yaroslav Rakitskiy made a pro-Ukrainian post on Instagram and severed his contract with the team.^[24][25] FIFA and the UEFA indefinitely suspended the team from their competitions.^[2] In addition, the European Club Association suspended the team.^[3]

On 30 April 2022, Zenit secured their fourth title in a row and eighth overall.^[26] Many of Zenit's foreign players have not been able to leave Russia, unable to secure moves away from Russian clubs, due to international sanctions placed upon the country as a result of Russia's invasion of Ukraine. ^[27]

On 7 May 2023, Zenit secured their fifth title in a row and ninth overall.^[28]

In 2024, Zenit was one of the organizers of the Equality Cup, an international football tournament.^[29]