The balanced scorecard (BSC) is an accepted methodology for putting strategy into action. The BSC provides a comprehensive performance measurement for an organization with respect to both financial and non-financial perspectives, including the triple bottom line of planet, people, and profit. Through various implementations to companies, organizations, and sectors, balanced scorecards have been used widely both for strategic purposes, as well as for more tactical focus for auditing current performance. BSC implementation is particularly adequate when integrated with the operational processes of the organization. The integration between the strategic plan and the financial and operational plans proceed via the business process model that covers the operational processes associated with the objectives of the organization in the strategy map. In this way, BSC is a tool for real-time monitoring of performance as well as providing the crucial linkage to the organization’s strategy that enables the proper implementation of the organization’s strategy. Data envelopment analysis (DEA) has been widely applied for measuring the efficiency of a specific decision-making unit (DMU) against a projected point on an efficiency frontier. DEA is therefore particularly suitable for measuring the organizational efficiency based on the BSC indicators, which are defined as Key Performance Indicators (KPIs). In the commercial fisheries sector, sustainable strategy of fisheries organizations can be gained by running the current operations more effectively, and by integrating processes enabling adaptation to change. The efficiency frontier of the DEA model can be used to calculate the efficiency of fisheries operations. The proposed research is undertaken as part of the Canadian Fisheries Research Network (CFRN) to investigate the application of BSC and DEA for defining commercial fisheries performance evaluation variables with respect to the objectives of environmental sustainability, economic viability, and social and cultural stability in compliance with, and in the absence of, performance monitoring alleged in the Fisheries and Oceans, Canada Integrated Fisheries Management Plans (IFMP). The combination of BSC-DEA methodologies is developed in this research as a required performance monitoring system suitable for IFMPs for analyzing the relative efficiency of commercial fisheries case studies across Canada towards incorporating best sustainable practices in the industry.