Described herein are systems and methods for multiplexing pipelined data for backup operations. Various data streams are combined such as by multiplexing by a multiplexing module. The multiplexing module combines the data from the various data streams received by receiver module(s) into a single stream of chunks. The multiplexing module may combine data from multiple archive files into a single chunk. Additional modules perform other operations on the chunks of data to be transported such as encryption, compression, etc. The data chunks are transmitted via a transport channel to a receive pipeline that includes a second receiver module and other modules. The data chunks are then stored in a backup medium. The chunks are later retrieved and separated such as by demultiplexing for restoring to a client or for further storage as auxiliary copies of the separated data streams or archive files.