With the release of Age Ain't Nothing but a Number, rumors circulated of a relationship between Aaliyah and R. Kelly. Shortly after, there was speculation about a secret marriage with the release of "Age Ain't Nothing but a Number" and the adult content that Kelly had written for Aaliyah. Vibe magazine later revealed a marriage certificate that listed the couple married on August 31, 1994, in Sheraton Gateway Suites in Rosemont, Illinois. Aaliyah, who was 15 at the time, was listed as 18 on the certificate; the illegal marriage was annulled in February 1995 by her parents. The pair continued to deny marriage allegations, stating that neither was married.
Aaliyah reportedly developed a friendship with R. Kelly during the recording of her debut album. As she recalled to Vibe magazine in 1994, she and R. Kelly would "go watch a movie" and "go eat" when she got tired and would then "come back and work". She described the relationship between her and R. Kelly as being "rather close." In December 1994, Aaliyah told the Sun-Times that whenever she was asked about being married to R. Kelly, she urged them not to believe "all that mess" and that she and R. Kelly were "close" and "people took it the wrong way." In his 2011 book The Man Behind the Man: Looking From the Inside Out, Demetrius Smith Sr, a former member of R. Kelly's entourage, wrote that R. Kelly told him "in a voice that sounded as if he wanted to burst into tears" that he thought Aaliyah was pregnant.
Aaliyah admitted in court documents that she had lied about her age. In May 1997, she filed suit in Cook County seeking to have all records of the marriage expunged because she was not old enough under state law to get married without her parents' consent. It was reported that she cut off all professional and personal ties with R. Kelly after the marriage was annulled and ceased having contact with him. In 2014, Jomo Hankerson stated that Aaliyah "got villainized" over her relationship with R. Kelly and the scandal over the marriage made it difficult to find producers for her second album. "We were coming off of a multi-platinum debut album and except for a couple of relationships with Jermaine Dupri and Puffy, it was hard for us to get producers on the album." Hankerson also expressed confusion over why "they were upset" with Aaliyah given her age at the time.
Aaliyah was known to avoid answering questions regarding R. Kelly following the professional split. During an interview with Christopher John Farley, she was asked if she was still in contact with him and if she would ever work with him again. Farley said Aaliyah responded with a "firm, frosty" 'No' to both of the questions. Vibe magazine said Aaliyah changed the subject anytime "you bring up the marriage with her". A spokeswoman for Aaliyah told the Chicago Sun-Times in 2000 that when "R. Kelly comes up, she doesn't even speak his name, and nobody's allowed to ask about it at all".
R. Kelly would have other allegations made about him regarding underage girls in the years following her death and his marriage to Aaliyah was used to evidence his involvement with them. He refused to discuss his relationship with her, citing that she was deceased. "Out of respect for her, and her mom and her dad, I will not discuss Aaliyah. That was a whole other situation, a whole other time, it was a whole other thing, and I'm sure that people also know that." Aaliyah's mother Diane Haughton reflected that everything "that went wrong in her life" began with her relationship with R. Kelly. The allegations have been said to have done "little to taint Aaliyah's image or prevent her from becoming a reliable '90s hitmaker with viable sidelines in movies and modeling."