Using a knowledge-based theory of the firm within the larger framework of resource-based theory, this ongoing study examines how firm knowledge structures are disrupted under different modes of innovation. Building further on innovation management theory, it is proposed that e-business innovation must be analysed at two related levels: the business model level and systems level. Irrespective of whether business innovations are radical, modular, incremental or architectural, it is suggested that e-business systems-level innovation is systemically architectural. Relationships between the two levels of innovation and the influence of knowledge assets are also discussed. A triangulated method-based approach, the multi-case site, and ongoing progress is further reported.