Systems and methods for bypassing a compromised engine cylinder via cylinder deactivation are described according to various embodiments herein. A system includes an engine coupled to a controller. The controller includes at least one processor and at least one memory coupled to the at least one processor. The at least one memory stores instructions that, when executed by the at least one processor, cause the controller to: determine that one or more cylinders of a plurality of cylinders of the engine is compromised based on data regarding operation of the engine; and cause the engine to operate in the modified engine operating mode whereby operation of the one or more cylinders that are compromised is modified.