Establishing an organization, setting it on track of development is becoming a more and more complicated task and in most cases, requires expert knowledge. Scientific organizational theory offers a great variety of applicable methods and tools for small and young enterprises as support for their design and development. The performed case study is based on consultancy work at local Business Incubator in Subotica. This article presents the author's approach, examination and description of some of the most common problems of small enterprises. A number of organizational theoretical terms were considered and have been connected with the specific case. The basic aim of the project was to solve a set of actual organizational problems for one of the business incubator tenants. The analyzed group of problems were related to the structural design of an organization (e.g. existing simple structure vs. functional), division of labor, job design, decentralization, delegation, formalization and standardization, and span of control. The applied methods were based on classical organization theory, contingency theory, Adizes life cycle of organizations, and other different partial approaches. Far from the full set of factors that an up-to-date contingency survey uses, this article considers only a few aspects with special focus on small enterprises and their typical symptoms. While the task was successfully completed, it seems this combined approach lends proof to the problem solving possibilities of such methodical approach of applying organizational theoretical knowledge in practice.