Interoperability is one of the most challenging issues in the design and operation of large-scale computing infrastructures for multidisciplinary research. It requires solutions that can “embrace” heterogeneity, i.e. accommodate multiple incarnations of similar resources, as well as “hide” it, i.e. provide consumers with a homogeneous view of diverse resources. This paper overviews the measures put in place in the D4Science infrastructure to address a range of interoperability problems.