The couple welcomed the baby girl, their first child, on Saturday (January 7) at New York's Lenox Hill Hospital.
According to The New York Daily News, Beyoncé and Jay-Z checked out of the hospital at approximately 1.30am on Tuesday morning.
They are said to have exited via the facility's side entrance in a van with blacked-out windows and were accompanied by a procession of two SUVs.
"[It was] very precise, very military-like," a witness told the publication. "Immediately, security personnel began leaving the hospital."
Beyoncé and Jay-Z revealed that Blue Ivy was delivered naturally earlier this week, dispelling rumours that the 'Countdown' singer had undergone a scheduled C-Section.
A spokesperson for Lenox Hill Hospital recently denied taking a $1.3m (£840,000) payment to shut off part of the facility for Beyoncé and Jay-Z after it was reported that the celebrity couple had rented the entire Labour and Delivery Suite.
Watch the video for Beyoncé's 'Love On Top' below: