1. A system for managing document conversions, comprising: at least one server computer communicatively coupled to one or more devices on a network and running an isolation service configured for: first determining whether a native application associated with a native document type is already executing when a document having the native document type is ready for conversion, ensuring only a single instance of the native application executes for the conversion; causing the native application to load and convert the document to a new document format; and managing the conversion of the document by the single instance of the native application according to at least one specified document conversion operation parameter, condition, or setting.