Messi was nominated for the UEFA Best Player in Europe Award, along with Cristiano Ronaldo and Franck Ribéry, for a third consecutive year.^[163] Ribéry won the award with 36 votes. Messi finished in second place with 14 votes, while Ronaldo finished in third-place with 3 votes.^[164][165] On 18 August 2013, Messi opened the2013–14 La Liga Season with two goals and an assist against Levante UD, as Barcelona went on to win the match 7–0.^[166] On 28 August, Barcelona claimed their eleventh Supercopa de España title over Atlético Madrid on away goals.

On 1 September, Messi scored his twenty third career hat-trick in a 3–2 win against Valencia CF. With these goals he became the player to score 100 away goals and become highest scorer in away fixtures in the league's history.^[167] These goals made him the sixth-highest goalscorer in the history of La Liga, surpassingQuini's tally of 219.^[168][169] On 18 September 2013, Messi scored his 24th career hat-trick in Barcelona's first Champions League win of the season, at home against Ajax, which ended 4–0. The goals made him the second-highest goalscorer of all time in the Champions League, with 62 goals, only behind Raúl, and the fourth-highest goalscorer of all time in European Competitions, with 63. With this hatrick Messi became the first player to score four hat tricks in the Champions League.^[170] On 10 November, Messi suffered an injury in a 4–1 away win against Real Betis, which would keep him sidelined until January 2014. This was his third injury of the season.^[171]

On 8 January 2014, Messi returned from injury to score twice for Barça in a 4–0 Copa del Rey win against Getafe.^[172] On 13 January, he placed second in the 2013 FIFA Ballon d'Or, behind Cristiano Ronaldo.^[173] On 15 February, Messi scored twice against Rayo Vallecano in a 6–0 win to overtake fellow Argentine Alfredo di Stéfano and draw level with Raúl as the third-highest goalscorer in La Liga history with 228 goals.^[174]

On 16 March 2014, Messi scored a hat-trick in a 7–0 defeat of Osasuna to overtake Paulino Alcántara as Barça's top goalscorer in all competitions, includingfriendlies.^[175] On 23 March, he scored a hat-trick in a 4–3 win against Real Madrid at the Santiago Bernabéu to become the outright all-time top goalscorer in El Clásico fixtures, ahead of Di Stefano.^[176] These goals also enabled him to become the second highest goalscorer in La Liga, overtaking Hugo Sanchez.^[177]

Messi finished his club season with only one trophy, the Spanish Super Cup, as Barcelona finished as runners-up in La Liga, behind Atletico Madrid, who had also eliminated them in the quarter finals of the Champion's League that season. Barcelona were also defeated in the Copa del Rey final by rivals Real Madrid, although Messi was the top scorer in the competition. Messi concluded the season with 41 goals and 15 assists in all competitions, but his 28 league goals in La Liga were not enough for him to defend the Pichichi trophy, which went to Cristiano Ronaldo, who managed 31 goals.^[178] On 16 May 2014, Messi agreed a new contract with theCatalan club.