An integrated circuit may have pipelined programmable interconnects that are configured to select between a routing signal stored in storage nodes of a pipeline element and the identical routing signal bypassing the pipeline element. A programming element may access the storage nodes of the pipeline elements for write operations and, if desired, for read operations. For example, the programming element may perform write operations to initialize the storage nodes to a known state during power-up operations or to reset the pipeline element. In addition, the programming element may perform reed operations for debug and testing purposes.