The results of this research represent an important contribution to the scientific literature that deals with the study of innovative startup ecosystems and startup companies. The research involves collecting data on founders and startup companies as leading participants in the innovative startup ecosystem. Startup companies have an essential role in encouraging all other participants in the direction of innovation development and implementation of innovative activities. For this research, an original measuring instrument was created as a questionnaire that examines the development factors of the innovative startup ecosystem. The research provides a detailed insight into the profile and operations of startup companies within the innovative startup ecosystem. Examining the individual and joint impact of development factors of the innovative startup ecosystem on startup companies is made possible by using different statistical methods. The factors were grouped into the following units: factors that influence the founder’s decision to invest and launch a startup company, general factors that influence the functioning and sustainability of the innovative startup ecosystem, and risk factors that influence the growth and development of the startup company in the innovative startup ecosystem. According to the research carried out as part of the doctoral dissertation, the founder’s decision to invest and launch a startup company mainly depends on the factors such as the influence of costs, financing conditions, and demand for a product or service. The most important general factors influencing the functioning and sustainability of the innovative startup ecosystem are administrative conditions for business, entrepreneurial culture in the innovative startup ecosystem, legal solutions in the field of startup companies, and social events (e.g., networking, gatherings, etc.). The research also determined the main risk factors that most affect the growth and development of a startup company in the innovative startup ecosystem: the risk of the ability to expand the business and the risk of procurement. In addition to determining the most critical factors of the development of the innovative startup ecosystem, their grouping into appropriate dimensions was performed using appropriate statistical analysis. Connecting these dimensions with startup companies in the innovative startup ecosystem and examining their relationships significantly contributes to quantitative research in this area and creates good foundations for future research.