Since Hamilton proposed quaternions as a system of numbers that does not satisfy the ordinary commutative rule of multiplication, quaternion algebras have played an important role in many mathematical and physical studies. This paper introduces the generalized notion of Pauli Fibonacci polynomial quaternions, a definition that incorporates the advantages of the Fibonacci number system augmented by the Pauli matrix structure. With the concept presented in the study, it aims to provide material that can be used in a more in-depth understanding of the principles of coding theory and quantum physics, which contribute to the confidentiality needed by the digital world, with the help of quaternions. In this study, an approach has been developed by integrating the advantageous and consistent structure of quaternions used to solve the problem of system lock-up and unresponsiveness during rotational movements in robot programming, the mathematically compact and functional form of Pauli matrices, and a generalized version of the Fibonacci sequence, which is an application of aesthetic patterns in nature.