Barcelona signed a five-and-a-half year shirt sponsorship deal worth up to 170 million euros ($225 million) with the non-profit Qatar Foundation in December touted as the largest sponsorship deal in football history.
But the club's decision to collect money for the first time in its history to display a logo on its jerseys did not go down well with many fans who have pressured Barcelona's board to re-think the deal at a meeting on Saturday.
Barcelona's legendary former Dutch coach Johan Cruyff has blasted the endorsement deal as "vulgar" while former club president Joan Laporta has said he would prefer to see the jerseys carry only the logo of UNICEF, an image which has "a message, a cause".
Guardiola, who played for Qatar's Al Ahly between 2003 and 2005 and who was one of the ambassadors for the nation's successful 2022 World Cup bid, has stepped into the debate in comments published on the club's official website.
"I can tell you that I lived for two years in Qatar and my family and I received wonderful treatment," the 40-year-old said.
"These are difficult times and the board has the obligation to search for alternatives. Qatar is the most open Muslim country and the closest to the Western democracies, but they need time".
Guardiola concluded by saying: "If the members decide to continue, then we will still have the sponsorship of a foundation which is doing things for research and for culture. If not, then we will move ahead with different resources. Whatever happens, the players will continue to run and fight, which in the end is the most important thing".
The Qatar Foundation, founded in 1995, has set up projects focusing on education, scientific research and community development, mainly in the Middle East.
It is run by the wife of Qatar's Emir, Sheikh Hamad bin Khalifa al-Thani who seized power from his father in a bloodless coup in 1995 and in 2003 declared his son Tamim heir apparent.
Part of the opposition to the shirt sponsorship deal stems from the lack of democracy in Qatar, which has no organised opposition groups and where parliamentary elections have repeatedly been postponed.
Thousands of Barcelona fans have signed a petition to demand that the agreement be revoked and the club's board decided to let representatives of club members to decide on Saturday if the deal will remain in place.