Bhardwaj had read a short version of William Shakespeare's Macbeth and wanted to turn it into a gangster film. He had seen Akira Kurosawa's Throne of Blood (1957), which was also inspired by Macbeth. It inspired Bhardwaj to make it into a feature film. He then started working with Abbas Tyrewala to adapt the play. Bhardwaj then came up with its film adaptation Maqbool (2003), starring Pankaj Kapur, Irrfan Khan and Tabu; it was set against the backdrop of Mumbai underworld. The film was screened at the 2004 Cannes Film Festival and at the 2003 Toronto Film Festival. Sita Menon of Rediff.com in her review called it "..a visual gallery that is an intelligent blend of dark, tragic overtones and comic, satirical undertones." CNN-IBN listed Maqbool as "one of the 100 greatest Indian films of all time" in a 2013 list. In 2010, Film critic Raja Sen mentioned it in "The Top 75 Hindi Films of the Decade" list.
In 2013, Bhardwaj directed Matru Ki Bijlee Ka Mandola, a political satire set in the rustic surroundings of a village in Haryana. It starred Anushka Sharma and Imran Khan in the lead roles, with Pankaj Kapur and Shabana Azmi in supporting ones. Bhardwaj also choreographed a song "Oye boy Charlie" in the film. The film received mixed reviews from critics, and underperformed at the box office.