The Catalan club decided to spend around £124m to sign the French winger from Borussia Dortmund; however, the 24-year-old has endured a difficult spell at Camp Nou, largely due to injury.
Although Barca had the option to sign Mbappe, Bartomeu is adamant that it was not his decision to recruit Dembele, who could leave the club for free next summer when his contract expires.
"[Mbappe's] signing was on the table, but the coaches preferred Dembele because they wanted a player to open the field," Bartomeu said on Catalan TV channel Esport3.
When speaking about other signings the club has made, including Philippe Coutinho in 2018, the 58-year-old added: "Some of the transfers we have done have not met expectations, players who have cost a lot of money, but these things happen in football.
"When those two players were signed (Dembele and Coutinho), they were applauded by everyone. Coutinho came because [Andres] Iniesta was going. He was the best in the Premier League. Dembele came because of Neymar's departure."
Dembele has made 118 appearances for Barcelona since joining the club four years ago, scoring 30 goals and providing 21 assists, while Mbappe has found the net 137 times and has laid on 67 assists in 183 appearances for Paris Saint-Germain in the same period.