Embedded boundary scan testing apparatus and methodologies are disclosed for testing processor-based circuit boards without processor intervention. A boundary scan controller is embedded in a circuit board along with a boundary scan chain having JTAG devices connected with an electrical circuit of the board. Upon power up, the boundary scan controller holds an on-board processor system in reset, loads boundary scan test vectors and commands from an on-board non-volatile memory, and runs boundary scan testing while holding the processor system in the reset state. The boundary scan controller preferably includes a test access port controller that implements only a subset of the JTAG standard 16 machine states to optimize performance and minimize controller hardware. The test results may be stored in an externally accessible on-board memory for subsequent retrieval in order to facilitate board troubleshooting and/or repair, where the provision of on-board boundary scan testing allows testing of boards while installed in the field, and the embedded scan controller allows field testing of on-board processor systems and related circuitry to enhance the test coverage over processor-driven boundary scan testing.