Methods and systems for selective encryption and secured extent quota management for storage servers in cloud computing are provided. A method includes associating at least one secure storage disk and at least one non-secure storage disk to a virtual disk, and associating the virtual disk to an application to allow access of the at least one secure storage disk and the at least one non-secure storage disk. The method further includes accessing the at least one secure storage disk and the at least one non-secure storage disk based on the associating of the virtual disk to the application, to write or read confidential and non-confidential data associated with the application into a respective one of the at least one secure storage disk and the at least one non-secure storage disk.