The bus bays, streetcar platform and fare gates are located at street level.

The station was initially built with its turnstiles and collector booths on the concourse level between the bus and streetcar terminal and the subway platforms, because until 1973, some of the buses serving the station crossed the fare zone boundary between Toronto and the then-city of Scarborough.

Main–Danforth has been identified by Metrolinx as a transportation mobility hub as it is located at the interchange of two or more current or planned regional rapid transit lines.

[7] As a result, Main Street was the first subway station to be outfitted with new accessible paddle-style Presto fare gates, which replaced the existing tripod turnstiles system-wide and are used with Presto cards[8] across the subway system.

The TTC closed the bus and streetcar loop at Main Street station between May 7, 2023, and September 2023 for infrastructure upgrades.

The work included concrete and asphalt pavement rehabilitation within the bus loop, concrete bus platform rehabilitation including the installation of tactile walking surface indicator, and fencing replacement throughout the loop.

To the west the subway tunnel was mostly constructed by cut-and-cover along Harris Avenue from Woodbine station.