Malik was raised as a Muslim and speaks English and Urdu, and can read Arabic.
In the past he has been a target of anti-Muslim attacks . During the 2014 Israel–Gaza conflict, Malik posted the message "#FreePalestine" on Twitter, resulting in him receiving angry responses and death threats. In 2017, Malik said he identified as a non-practising Muslim, but said he did not "want to be defined by [his] religion or [his] cultural background." He told British Vogue in November 2018 that he no longer considered himself a Muslim.
Malik started dating fellow X Factor contestant Geneva Lane of Belle Amie in 2010 until 2011. Malik then dated another X Factor contestant Rebecca Ferguson for a few months until July 2011. He subsequently dated actress Stephanie Davis in the same year. Malik began dating English singer Perrie Edwards of the band Little Mix in December 2011. They got engaged in August 2013, before breaking up in August 2015. Malik has been understood as the subject behind Little Mix's 2016 hit single Shout Out to My Ex.
Malik has been in a relationship with American model Gigi Hadid since late 2015. Hadid starred in his music video for the song "Pillowtalk". The two appeared together on the August 2017 cover of Vogue. In 2017, Hadid photographed them both for a Versace ad campaign. Malik and Hadid welcomed their first child, a daughter, in September 2020. The family spend a majority of their time in their home on a farm in rural Bucks County, Pennsylvania, where Hadid's mother and sister also own land. Malik also owns an apartment in SoHo, Manhattan.
Malik is a lifelong supporter of Bradford City A.F.C.