System Prompts Under the Hood: How LLMs Learn to Follow Instructions

System prompts define how LLM agents behave, use tools, follow policies, and prioritize instructions. Understanding how they work under the hood helps developers write better prompts, evaluate them systematically, and reduce security risks such as jailbreaks and prompt injection. This article covers how LLMs see system prompts, how they are trained to follow instructions, and what consequences this has.