Core competencies are major drivers behind the success of many Small and Medium sized organizations (SMEs). While Information Technology (IT) can be leveraged to enhance these competencies, changes in IT and poor planning may result in core rigidities. Many SMEs experience difficulties in planning and aligning IT applications with business objectives and core competencies and limited scientific studies have been conducted to assist SMEs in this regard. The present study examined the alignment of IT applications with non-technological competencies in South Africa and Uganda. It sought to identify those configurations of IT applications and non-technological competencies that result in IT-based competencies needed to ensure competitiveness in e-commerce in the SME sector. The perspective of alignment as a gestalt was adopted. 112 SMEs were surveyed and three alignment configurations consisting of SMEs with innovative IT competencies; Operational IT competencies and adaptive IT competencies were revealed. SMEs with innovative IT competencies developed the most IT-based competencies. They achieved this by leveraging various operational and strategic IT applications to enhance a number of non-technological competencies.