The measured above average rate of the Entrepreneurial Employee Activity (EEA) is a hidden and unused component of the entrepreneurial potential of Croatia. Since EEA refers to innovative activity aimed at development of new products/services or establishing new business units, it can be used to stimulate the necessary development of new products in corporate structures. EEA stimulates growth and profitability of companies and allows for positive macroeconomic outcomes. It has proven to be particularly favourable for the economic growth and development of countries in transition. The aim of this paper is to research impacts of macro and micro business ecosystems on EEA in order to stimulate it and in such a way contribute to innovation and sustainable competitiveness of Croatian economy. The interconnection of micro and macro business ecosystems and EEA was analysed in a qualitative research (interviews and focus groups) using a sample of sixteen businesses, eight of which from IT industry and eight from processing industry. It was established that business ecosystems differ depending on the type of industry and that they shape organisational factors which influence the EEA. Based on the research results it is assumed that businesses can stimulate entrepreneurial activity of employees by creating a suitable organisational structure and culture and implementing a business policy adapted to the macro ecosystem. Based on this assumption, micro level proposals for stimulating EEA are presented.