He previously played for Ashanti Gold, Free State Stars, Granada, Evian, Anzhi Makhachkala, Columbus Crew, San Jose Earthquakes, and New England Revolution.

Born in Accra, Jonathan began his professional career in his native Ghana with Ashanti Gold, but departed after one season to join Free State Stars in South Africa.

[2] After coming through the academy setup at Ashanti Gold, Jonathan was handed his professional debut for the club by head coach David Duncan during the 2007–08 Ghana Premier League season.

[4] Jonathan joined South African club Free State Stars in September 2008, moving to Ea Lla Koto alongside his 'AshGold' teammate David Telfer.

At the end of the season, Jonathan received a trial with Greek club Panathinaikos; he was "reported to have done well," but could not sign for the team since they had exhausted their quota of foreign players.

Both clubs submitted offers to Free State Stars, but it was Udinese who brought the player in for a medical in late December, ahead of the opening of the transfer window on 1 January.

[10] With the opening of the Italian transfer window, Jonathan officially became an Udinese player on 1 January 2010; he signed a three-year contract with the Serie A club.

In Italy, both Juventus and Lazio registered interest in the player, while reports from his native country suggested that Premier League clubs Aston Villa and Tottenham Hotspur would pursue a transfer.

The initial loan to the Segunda División B side was for six months, in order to get him regular playing time; it was also necessary because Udinese already had hit their quota of foreign players, and were unable to register Jonathan in the squad.

On 8 July 2011, Jonathan moved to newly promoted Ligue 1 side Evian, signing a four-year contract with the French club for an undisclosed fee.

[26] Jonathan returned to the first team in 2013, featuring in Evian's opening game of the 2013–14 Ligue 1 campaign and playing the full ninety minutes in a 1–1 draw with Sochaux on 10 August 2013.

Following his performances at the 2014 FIFA World Cup, Jonathan was rated highly[31] and rumored to be a transfer target for "several big European clubs," notably Monaco[32] and Sampdoria.

Jonathan was a staple in the team at the start of the year, appearing ten times for Les Croix de Savoyes through the end of October.

During that stretch, he scored his second goal for the club in a 2–1 victory over Lens;[34] he also received his second red card in a 2–1 defeat to Lorient in the Coupe de la Ligue.

The case stemmed from his transfer to Evian in July 2011, as FIFA judged that Jonathan had still been under contract with Udinese but claimed to be a free agent when he signed with the French club.

[38] Udinese had originally reported him just weeks after the transfer, claiming that he had four years remaining on his contract; Jonathan, however, responded by saying "My manager cannot make such a mistake.

Following the CAS ruling, FIFA confirmed that the ban began retroactively on 30 April 2015, and "begins again at the start of the next season, whichever country he may choose to play in."

Four-time defending Scottish champions Celtic had shown interest in the player,[41] but promptly ended their pursuit following the announcement from FIFA confirming the ban.

On 23 February 2016, Jonathan signed a two-and-a-half-year contract with Russian Premier League club Anzhi Makhachkala;[46] according to reports, the transfer fee for the defender was just €150,000, with a 20% sell-on clause tacked on as part of the agreement.

[48] Jonathan missed much of the spring while on international duty, and returned to the club at the end of April with Anzhi sitting bottom of the table in the RPL.

He started each of the last three games of the season, from which Anzhi claimed seven points, helping the club advance to 13th and into a relegation playoff against Volgar Astrakhan of the Russian Football National League.

[51] Midway through the winter break, Jonathan was rumored to be departing Anzhi permanently, with American club Columbus Crew SC the reported destination.

[53] Prior to the season, Jonathan was named as part of the leadership council for the Crew, alongside Federico Higuaín, Ethan Finlay, Justin Meram, and Josh Williams.

Jonathan remained on the leadership council ahead of the 2018 season, this time joined by Ricardo Clark, Higuaín, Hector Jiménez, Zack Steffen, and Williams.

[64] He would see his contract bought down by the club in late January, meaning that Jonathan would no longer be considered a Designated Player and clearing the way for Milton Valenzuela to be acquired by Columbus.

[68] During the 2021 Columbus Crew season, Jonathan scored 4 total goals across all competitions; including the game winner versus Atlanta United FC on 24 July.

[69] On 10 February 2023, the San Jose Earthquakes announced they had acquired Jonathan from the Columbus Crew for a fee of $200,000, possibly rising to $500,000, depending on his longevity with the Quakes.

[70] On 4 January 2024, Mensah reunited with former head coach Caleb Porter at New England Revolution, who he joined as a free agent after leaving San Jose at the end of their 2023 season.

[89] Two years later, at the 2017 Africa Cup of Nations, Jonathan was initially named to the preliminary squad on 2 January;[90] one day later, he left camp to complete a transfer move to Columbus Crew.