An architecture for an integrated circuit with in-circuit programming allows real-time modification of the in-circuit programming code and other code stored on the chip. The architecture utilizes a microprocessor and control logic on an integrated circuit having a single non-volatile memory that stores instructions and data, such as in-circuit programming and user code, and input/output ports and related structure for exchanging data with an external device. Using in-circuit programming code stored on the chip, the chip interactively establishes an in-circuit programming exchange with an external device to update data and instructions including the in-circuit programming code. Input/output conflicts during in-circuit programming can be avoided by employing a memory controller to handle at least part of the in-circuit programming operations. The memory controller allows the in-circuit programming code to be updated in real time.