On December 17, 1995, the Morristown & Erie's wholly-owned subsidiary, the Bayshore Terminal Company, began providing contract switching services in the Bayway Refinery, currently owned by Phillips 66 (originally Tosco and later Conoco-Phillips). The M&E also serves Infineum, which was formerly Exxon Chemicals' Paramins division, as well as Chemours (formerly DuPont) and Eastman/Solutia (formerly AirBP).

In addition to serving the existing in-plant customers, Conoco-Phillips completed a polypropylene manufacturing plant in 2003. It was designed for rail service and rail access to the plant. It has a 450-car receiving yard that was constructed so the M&E could efficiently serve this new facility.

The Bayshore Terminal Company has two locomotives, a permanently assigned trainmaster, and a three-man train crew to support operations seven days a week, 365 days a year. A safety coordinator is on call at all times, and spends at least two days a week at the refinery.