You need the embedded coder to convert the Simulink models for using on an embedded system. If it is a famous hardware platform, there is usually a support package available that provides Simulink blocks to configure and control I/O pins. For example, Raspberry pi has a support package: https://www.mathworks.com/help/supportpkg/raspberrypi/index.html?s_tid=CRUX_lftnav, which shows how to upload the program from Simulink to the board. This support package requires that you have an OS already installed on the board.
If you are interested in bare-metal programming, then Simulink also has support packages for STM32 processors and boards: https://www.mathworks.com/hardware-support/stmicroelectronics.html and TI processors: https://www.mathworks.com/hardware-support/texas-instruments.html.
If any support package does not support a processor, you will most probably need to use S-function blocks and at least write the C code to control the pins.
