According to aspects illustrated herein, methods and systems for retaining duplex scanning information in a scanned output file, is disclosed. The method includes receiving a document for scanning, having multiple pages, wherein each page has a first side such as a front side and a second side such as a back side. Then, a check for selection of a duplex scanning feature by a user, is performed. Upon scanning, an image data representing an image of the document is generated. The image data and the duplex scanning feature selected by the user is processed to generate a scanned output file. The duplex scanning information is generated, while generating the scanned output file. The duplex scanning information is retained in the scanned output file, for later retrieval and use. The duplex scanning information helps identify the first side and the second side in the scanned output file.