[5][6][7] Construction was slightly stalled due to delays in the delivery of steel flues for the ventilation system.

[4]: 141 [11] In 1937, the IND Crosstown Line was connected to the station, served by the GG train (today's G service).

[20][21][22] Signals and switches at the station were replaced and modernized after the fire,[13]: 20 [14]: 15, 20  and again in Fall 2008 when the relay room was rebuilt.

[13]: 20 [23]: 22 In July 2019, the MTA revealed plans to restore express service on the Culver Line between Jay Street and Church Avenue by mid-September 2019.

[28][29] Dark green I-beam columns run along the entire length of both platforms at regular intervals with alternating ones having the standard black station name plate with white lettering.

[14]: 5 [24][31] The lower level was abandoned afterward;[14]: 6 [24] trains rerouted via the express tracks during construction or service disruptions bypass the station towards Jay Street (northbound) or 7th Avenue (southbound).

[15][32] The tile was removed during renovations in the 1990s, leaving unpainted concrete and corrugated metal, old lights and signage (including original IND signs reading "BERGN" on support pillars), and modern Exit signs, none of which are in usable condition.

[14]: 6 [24] A study on implementing an F express variant on the Culver Line found that reopening Bergen Street's lower level for express trains had potential benefits, including relieving passenger congestion along the heavily used northern section of the line, but that the costs of reopening the lower level outweighed the benefits.

[13]: 24  When the station was used for express service, passengers would wait on the staircases to see which level the next Manhattan-bound train would arrive at.

[14]: 6  This currently occurs at the Delancey Street/Essex Street station where passengers wait to see whether a northbound F arrives on the lower level, or whether a northbound M arrives on the upper level, since both services operate local along the Sixth Avenue Line north of that point.

[36] Repairs to restore the lower level to operating conditions, as well as required upgrades to make the station ADA-accessible, are estimated to cost over $75 million.

Since restoring the lower level is prohibitively expensive, it is bypassed by F express trains, which resumed service in September 2019.

The lower level tracks can only be reached by trains running to or from Jay Street–MetroTech since they do not connect to the IND Crosstown Line.

[13][30]: Appendix D-1 [37] Both levels have a switch south of the platforms, allowing terminating trains to reverse direction.