In this chapter we use secure multiparty computation (SMC) to enable privacy-preserving engineering of inter-organizational business processes. Business processes often involve structuring the activities of several organizations, for example when several potentially competitive enterprises share their skills to form a temporary alliance. One of the main obstacles to engineering the processes that govern such collaborations is the perceived threat to the participants’ autonomy. In particular, the participants can be reluctant to expose their internal processes or logs, as this knowledge can be analyzed by other participants to reveal sensitive information. We use SMC techniques to handle two problems in this context: process fusion and log auditing. Process fusion enables the constituents of a collaboration to discover their local views of the inter-organizational workflow, enabling each company to re-shape, optimize and analyze their local flows. Log auditing enables a participant that owns a business process to check if the partner’s logs match its business process, thus enabling the two partners to discover failures, errors and inefficiencies.