Development trends in management and organizational structures are considered one of the limitations of the ongoing transformation of the company architecture of enterprises in the Czech Republic. This study is based on the survey data of over 450 enterprises in different sizes and sector categories conducted in 2016 2019. Statistical dependence between the type of organizational structure and size of an enterprise is confirmed with a trend of transition to a department-based organizational structure at the expense of a division-based structure. A high degree of statistical dependence is found between the number of management levels and size of a company. However, a low level of statistical dependence is found between the number of management levels and the sector type. Dependence between management structure/size of an enterprise and its profitability is not confirmed. A critical strategic task for companies is acceleration of the transformation of the company architecture, including the organizational framework, and intensification of the innovation and digitalization based on a transfer of new knowledge into corporate practice. If enterprises accomplish this strategic task, they will generate higher value and they can be more profitable and sustainable. A transfer from classical management structures to departmental structures is demonstrated, which creates preconditions for transformation in process and project management. A new finding is an independent relationship between management structure/ size of an enterprise and its profitability; and an opposite trend considering the number of management levels compared to the prediction, i.e., their decrease.