Although today the importance of interdisciplinarity is widely recognized and the associated philosophical reflection is consolidating into an autonomous field of research, there is still no adequate understanding of what interdisciplinary projects consist of, nor are there clear agreements on how to execute them. Here we propose that the concept of boundary work, carefully adapted to the different contexts of scientific work, can shed light on how disciplinary structures are produced and therefore how interdisciplinary practices intervene in these processes. Along this line, we claim that a philosophy of interdisciplinarity must include an epistemology of boundary work, which allows for establishing criteria on the necessity and conditions of disciplinary integration for different pragmatic contexts: Scientific conferences and journals, educational programs, and research teams are considered. Additionally, we focus on how the concept of interdisciplinarity is used to loosen boundaries, and how researchers should be able to adapt their boundaries to different contexts and moments to avoid stagnation or loss of rigor. In order to illustrate our arguments, we take the interdisciplinary area of the National System of Researchers in Mexico as a case of a flexible boundary, and the Argentine Society of Neurochemistry as a case of a rigid boundary. [Note: The page range (133-152) shown in the citation is incorrect. The correct page range is 133-151.]