In the context of the global crisis in the economy enterprise and commercial companies are facing increasing competition in the market, the decline in consumer demand, changes in external market conditions. To the management raises the question of effective crisis management. The increasing competition leads to the need to solve the following questions: efficiency of decision making, customer orientation, dependence on the «human factor», the satisfaction of employees. Methodology of a comprehensive reengineering business processes can provide the company with a new business model, based on the economic strategy of the company in crisis. The result of redesigning of all business processes in organization may be new, resistant to sudden changes in the external environment and ensure effective decision making under conditions of high uncertainty, the business enterprise architecture. The article describes the methodology of the phased re-engineering of business processes for small and medium commercial companies, which relies on the establishment of an economic strategy and a review of the reference model. The purpose of reengineering business processes is determined by the preservation of the company's market share and profitability. The result of the redesign of the business processes of the organization becomes a new business model, expressed in the formulation of economic strategy, new organizational structure, new landscape scheme of business processes «to-be». In the article discussed questions of organization transition from current management models to a new business model. The introduction of a new management model and the new landscape of business processes allows companies to exclude «excess» business processes, thereby optimize the costs of organizational work. Reengineering business processes enables the company to achieve the goal of crisis management is to maintain market share and profitability of the business.