The rich body of physical theories defines the foundation of our understanding of the world. Its mathematical formulation is based on classical Aristotelian logic. In the philosophy of science the ambiguities, paradoxes, and the possibility of subjective interpretations of facts have challenged binary logic, leading, among other developments, to Gotthard Günther’s theory of polycontexturality. Günther’s theory explains how observers with subjective perception can become aware of their own subjectivity and provides means to describe contradicting or even paradox observations in a (...) logically sound formalism. Here we summarize the formalism behind Günther’s theory and apply it to two well-known examples from physics where different observers operate in distinct and only locally valid logical systems. Using polycontextural logic we show how the emerging awareness of these limitations of logical systems entails the design of mathematical transformations, which then become an integral part of the theory. In our view, this approach offers a novel perspective on the structure of physical theories and, at the same time, emphasizes the relevance of the theory of polycontexturality in modern sciences. (shrink)