He has recommended a provisional set up of a collective leadership of three senior leaders to oversee the city unit until the upcoming polls.
On his part, Deora is likely to move to New Delhi for a national role in the Congress.
According to an aide, Deora had expressed his desire to quit shortly after meeting outgoing Congress President Rahul Gandhi in New Delhi on June 26.
"The same was conveyed to Mallikarjun Kharge and K.C. Venugopal, General Secretaries, All India Congress Committee," a statement from Deora's office said.
Gandhi had submitted his resignation last month, triggering waves of protests and resignations from all over the country.
Deora, a former Union Minister, was appointed President of Mumbai Congress on the eve of 2019 Lok Sabha elections, replacing Sanjay Nirupam.
His move is seen as "an expression of solidarity and collective responsibility with outgoing Congress President Gandhi's resignation".
However, Deora organised and oversaw Gandhi's visit to Mumbai on July 4.
The time that he was given to prepare for the elections was too little and too late, said the aide.
Nevertheless, during his brief tenure, he united the rank and file of the party and put an end to identity politics in Mumbai Congress, in the hope that the party once again returns to its multilingual, multicultural and socio-economically inclusive ideals.
The party, under his leadership, gave a decisive fight to the BJP-Shiv Sena combine in Mumbai, the statement said.
"In spite of many constraints, including his own election campaign, Deora was able to support Lok Sabha candidates to put up a strong fight.a"
Deora reiterated that he was "always available to serve the party as a trusted and resourceful lieutenant and looks forward to playing a more important role nationally".
He added that political realities have changed since 2019 results and all have to get ready for roles that these times demand.
( With inputs from IANS )