In high technology industries firms use strategic learning alliances to create value that can’t be created alone. While they open their interorganizational membrane to gain new skills and competences, generate new products and services, accelerate development speed, and enter into new markets their idiosyncratic knowledge base may be impaired when knowledge related dysfunctions like the unintended knowledge transfer, asymmetric learning speed or premature closing occur. Within a value approach we examine the interplay of alliance coordination activities that enhance value creation, emerging knowledge related dysfunctions, and formal and organizational protections measures which shall safeguard firms intellectual crown jewels. We tested our hypotheses with a sample of 111 strategic alliances of young technology based Enterprises (YTBEs) with competing partners in high and key technology industries. Our findings suggest that a focal firm’s alliance management is well advised to intensely coordinate the alliance and to be aware of dysfunctional tendencies that erode alliance value. Since organizational protection measures could exaggerate dysfunctional effects they should be deployed very deliberately on a modest level. Formal protections measures, in contrast, seem to aggravate coordination activities’ value creation effect by setting behavioral guidelines. Moreover, an unsuccessful negotiation process of formal protection agreements may allow a deselection of partners that would not obey others intellectual property interests. Finally, we highlight theoretical and managerial implications that arise from these findings.