Most programmable logic devices use a variant of the JTAG protocol for ISP, in order to facilitate easier integration with automated testing procedures. Typically, chips supporting ISP have internal circuitry to generate any necessary programming voltage from the system's normal supply voltage, and communicate with the programmer via a serial protocol. Microcontrollers are typically soldered directly to a printed circuit board and usually do not have the circuitry or space for a large external programming cable to another computer. The other advantage is that production can always use the latest firmware, and new features as well as bug fixes can be implemented and put into production without the delay occurring when using pre-programmed microcontrollers. This may allow manufacturers to program the chips in their own system's production line instead of buying pre-programmed chips from a manufacturer or distributor, making it feasible to apply code or design changes in the middle of a production run.

The primary advantage of in-system programming is that it allows manufacturers of electronic devices to integrate programming and testing into a single production phase, and save money, rather than requiring a separate programming stage prior to assembling the system. Some ISP interfaces manage to achieve the same with just a single pin, others use up to 4 for implementing a JTAG interface.

In general, modern protocols try to keep the number of pins used low, typically to 2 pins. Almost all manufacturers of microcontrollers support this feature, but all have implemented their own protocols, which often differ even for different devices from the same manufacturer. There is no standard for in-system programming protocols for programming microcontroller devices. It also allows firmware updates to be delivered to the on-chip memory of microcontrollers and related processors without requiring specialist programming circuitry on the circuit board, and simplifies design work. In-system programming (ISP), or also called in-circuit serial programming (ICSP), is the ability of some programmable logic devices, microcontrollers, and other embedded devices to be programmed while installed in a complete system, rather than requiring the chip to be programmed prior to installing it into the system.

Atmel spi programmer