The disclosed computer-implemented method for managing application updates may include (i) recording network activity of a target application, (ii) recording an identifying attribute of the target application that is associated with a current version of the target application, (iii) determining, based on recording the identifying attribute, that the target application has attempted to update from a previous version of the target application to the current version of the target application, (iv) locating a portion of network activity that reveals how to manually update an instance of the previous version of the target application, and (v) perform, in response to locating the portion of network activity that reveals how to manually update the instance of the previous version of the target application, a security action to protect a user from a candidate security threat. Various other methods, systems, and computer-readable media are also disclosed.