The results of research on the problems of management of company’s economic security in terms of instability are presented in scientific work. The purpose of the article is to give justified recommendations on improving economic security control mechanisms on the basis of innovation. General scientific and specific knowledge of methods and techniques of economic phenomena and processes, analysis and synthesis, induction and deduction, methods of statistical analysis, the method of expert opinions, and other matching methods have been used in the study. The economic security of the enterprise is understood as a condition of its operation under conditions of normal (pre-planned) development, according to which (declared) mission, goals and objectives are realized. Crisis development challenges that are able to significantly affect the economic security of enterprises (corporate sector) have been generalized. The specified new economic risks and challenges that occur in conditions of instability have been specified: growing competition for access to economic resources (raw materials, financial, intellectual), artificial limitation of opportunities to enter the financial markets, recovery problems raiding (transfer of ownership by using corruption schemes), rapid (unpredictable) changes in the market environment, the spread of computer crime, complications of financial procedures. Ukrainian enterprises are still dependant from external conditions through significant concentration of the national economy. "Gaps" remain in the Ukrainian economy in the terms and amounts of financing investment and consumer demand, reinforcing disparities between aggregate supply and demand. Proposals on introduction of innovative technologies of Economic Security Management have been introduced. The necessity of taking into account additional indicators that reflect the impact on business processes associated with the effects of the crisis and action steps to restore the normal functioning of the economy have been justified: the level of progressivity of technologies; factor completeness; stability ratio of staff; level of legal security; the average destructive influence. With the economic crisis, it is appropriate, in our view, to pay special attention to monitoring the financial condition of the company and assessment of the basis of its general level of economic security, implying that the crisis primarily generalize the risks destabilizing the financial sector of enterprise.