The League One club were granted permission to build an initial 11,000-seater ground by Merton Borough Council in December 2015.
However, the plans were called in for review in March by Boris Johnson, who was then London's Mayor.
Khan has called for any information which challenges Merton's decision.
AFC Wimbledon, who currently play in Kingston, see a move to Merton and Plough Lane as a return to their spiritual home, as it is where the original Wimbledon FC played until 1991.
The Dons' plans to redevelop the current site of Wimbledon Greyhound Stadium could see the capacity of the proposed new stadium increased to 20,000, and include the construction of 602 residential units.
In a report published by the Greater London Authority, Khan indicated his preference to reverse Johnson's decision to review the application, and hand the decision back to Merton council.
Dons chief executive Erik Samuelson and councillor Stephen Alambritis, the leader of Merton Council, have welcomed Khan's move but Wandsworth Council have previously objected to the scheme.
A decision from Khan, who was elected London Mayor in May, is expected once all the responses to the consultation have been considered.
The original Wimbledon FC were forced to leave Plough Lane in 1991 following the publication of the Taylor Report, which, in the wake of the Hillsborough disaster, recommended that top-flight sides should play in all-seater stadiums.
They shared Selhurst Park with Crystal Palace until 2003 when they moved to Milton Keynes, having been given permission to relocate by an independent commission a year earlier.
The club were subsequently renamed MK Dons, while their old Plough Lane home became a residential development.
AFC Wimbledon, formed in 2002 in response to the relocation, have played all their home games at Kingsmeadow, which is also home to non-league Kingstonian.
They have won six promotions in the 14 years since their formation, reaching the third tier with a 2-0 victory over Plymouth Argyle in the League Two play-off in May.
AFC Wimbledon took over the leasehold of Kingsmeadow in March 2003 and have agreed to sell the ground to Premier League side Chelsea.
Mayor of London Sadiq Khan has begun a 14-day consultation period over AFC Wimbledon's planning application for a new stadium at Plough Lane.