The author prefers using array functions over `foreach` loops in PHP due to clearer communication of intent, encapsulation of functionality within the function, and reduced chances of side effects. Array functions like `array_map`, `array_filter`, and `array_reduce` are highlighted for their clarity and maintainability. While the author acknowledges that loops can be more efficient in certain cases, especially with large datasets or when manipulating multiple variables, array functions generally provide more readable and less error-prone code.