In recent years, a growing number of B2B e-businesses are adopting inter-organizational information systems (IOS). IOS enable and facilitate sharing of IT resources and capabilities between two or more organizations. Scholars also agree that information technology (IT) recourses and capabilities are critical for delivering business value of IT. Although, extant literature has mainly focused on the relationship between IT capabilities and firm performance, we believe that it is also crucial to understand the IT capability building processes and examine/explore mechanisms to build IT capabilities from existing IT resources. In this study, IOS application capabilities are proposed as the main factor in creating business value of IT in B2B environment. Moreover, we try to understand the nature of B2B patterns in cooperative relationship, which are likely to moderate the IT capability building process from IOS resources to IOS application capabilities. Research framework and hypotheses are proposed drawing from organizational learning theory and relevant literature. Our work aims to provide insights on how firms build IOS capabilities in cooperative inter-organizational relationships through strategic alignment between IOS resources and B2B patterns.