The COVID-19 pandemic is one of the biggest challenges facing modern society and business. In a dynamic crisis situation such as the current one, the forecasts for the impact of COVID-19 on the world economy and the development of individual business structures are changing. Business is facing more and more difficulties, and uncertainty and uncertainty are increasingly taking over global and economic life. The implementation of an anti-crisis policy based on innovation is becoming key to tackling the pandemic. The main objective of this study was to demonstrate the challenges of bio-enterprises during corona virus pandemic in Bulgaria and the opportunities they can draw to create innovation. A number of research methods and techniques for the tertiary and empirical part of the work were applied in the aim of realizing the objects and goals of the research – economical, statistical, mathematical, descriptive, comparative, monographic, graphical, questionnaire survey, etc. Initial contact and other basic information about all organic producers are collected from the official register of the Ministry of Agriculture and Food of the Republic of Bulgaria – a database of producers, processors and traders of organic products and food produced in organic production in a way that maintains such an up-to-date database. The analysis is based on data processing by 234 surveyed representatives of bio-enterprises from all sectors of the bioeconomy in Bulgaria. The data analysis result shows that many small and large businesses are suffering challenges and this unprecedented coronavirus crisis has caused destruction for many businesses in the globe and it is challenging to survive with reduced revenue, jobs lost and life slowing down and weak marketing performance even difficult to keep a calm head and their business alive. To support these businesses the government should use different mechanisms by cooperating with wealthy peoples and other non-governmental organizations. Besides, the bio- business owners should manage expectations and communicate with staff, suppliers, banks, and customers throughout this coronavirus frightening. Reduce expenses, be open to their employees about their finances and keep marketing, use different alternatives to deliver their product and recover from the crisis. The changes in the production and economic activity as a result of the imposed measures for limiting the infection have been studied; the main risks threatening future development and the type of anti-crisis innovative decisions taken by management.