The disclosed computer-implemented method for replicating computing system environments may include (1) identifying each application installed on a plurality of computing systems, (2) creating, within a virtual machine image, virtual containers that store each application installed on the plurality of computing systems, (3) determining that a potentially malicious file is directed to a target computing system within the plurality of computing systems, (4) identifying each application installed on the target computing system, (5) in response to determining that the file is directed to the target computing system, replicating a configuration of the target computing system within the virtual machine image by, for each application installed on the target computing system, activating a virtual container that stores the application, and (6) determining how the file would affect the target computing system by sending the file to the virtual machine image and analyzing how the file impacts the virtual machine image.