Sania Mirza,s tennis cloth wears on the tennis court has drawn criticism from some Muslim religious groups. Muslim scholars had issued a ruling, saying that her skirts and T-shirts were "un-Islamic" and "corrupting". Jamiat-ulema-e-Hind rejected rumors about disrupting her game saying that they do not stop anyone from playing, although they found female tennis players' dress code objectionable. Nevertheless, Calcutta police tightened security measures to protect her. A leading cleric issued a religious order demanding that Mirza stop wearing indecent clothes to play tennis. The board ruled that she should wear long tunics and headscarves instead of standard-issue T-shirts and skirts. Mizra told the New York Times in 2013 "I remember having a thousand people for security. I couldn't leave the hotel room without informing about five different people. And even when I did, I had a car in front of me and I had a car behind me. I had a guy sitting with me." Nothing happened in Kolkata, but that was far from the last time that Mirza would be at the center of a media firestorm.
After Mirza spoke at a conference on safe sex in November 2005, some groups said she was a "corrupting influence on the youth." Mirza clarified her stance by saying that she was opposed to pre-marital sex.
Sania accused the All India Tennis Association (AITA) of using her as 'bait' in Paes-Bhupathi 2012 Olympics controversy.
In 2006, some newspapers reported that Mirza declined to play doubles with Israeli tennis player ShaharPe'er for fear of protests from India's Muslim community. However, she teamed up with ShaharPe'er for the 2007 WTA Tour of Stanford, California.
Mirza was pictured resting her feet and showing the soles of her bare feet as she watched compatriot Rohan Bopanna play in the 2008 Hopman Cup, with an Indian flag in front.She faced possible prosecution under the Prevention of Insults to National Honour Act.
Sania Mirza, along with Sunitha Rao were photographed violating the dress code at Beijing Olympic Opening Ceremony parade in 2008.
On 4 February 2008, Mirza said that she would stop appearing in tennis tournaments held in India, starting with the 2008 Bangalore Open the following month, citing the series of controversies and upon advice by her manager. But Mirza chose to participate at the 2010 Commonwealth Games in Delhi.
After both Mahesh Bhupathi and Rohan Bopanna refused to play in the men's doubles event at the 2012 Olympics with Leander Paes, Paes demanded that he be partnered with Mirza for the mixed doubles event. Mirza accused the All India Tennis Association (AITA) of using her as 'bait' to keep Paes happy as she wanted to play with Bhupathi, with whom she has won 2 grand slams. In the end, Mirza was paired with Paes and the pair lost in the quarterfinals of the mixed doubles.
Mirza was photographed without the Indian flag at the opening ceremony of the London 2012 Olympics. In response, Mirza reaffirmed her loyalty to the land of her birth – "To see the national flag go up while standing on the podium is the proudest moment in an athlete's life and I will want to experience that for myself in London."
Mirza was referred to as “Pakistan’s daughter-in-law” and unfit to be a representative of an Indian state after she was appointed the Telangana state's brand ambassador. The comment referred to Mirza's husband, Shoaib Malik is a Pakistani cricketer. Telangana chief minister KalvakuntlaChandrashekar Rao presented Mirza with INR 1 crore on two separate occasions while badminton player Saina Nehwal complained that she did not receive the prize money promised to her for winning the Olympics bronze medal. However, the issue was immediately addressed by the government of Telangana.