The paper is aimed at the innovation process in the context of the business portfolio of micro-enterprises. This type of companies is typical of and prevalent in the southern region of the Czech Republic, and the presented conclusions have general validity. A newly developed method of assessing the innovative technological potential of enterprises called "Business technology assessment system" (BTAS), with the contribution of "Criteria analysis of systems". The research answers the question, what economic efficiency can innovations in the production process bring to SMEs dealing with custom manufacturing in the engineering sector. Technological backwardness including corporate infrastructure was proven. Companies compensate for this shortcoming by an increased focus on satisfying customer needs and a high degree of flexibility and innovation in production. From the point of view of production processes, there is a high degree of interconnectedness between individual operations and sub-processes. The business portfolio of most of these companies is disproportionately broad, and this is reflected in the negative findings in terms of the disproportionate number of methods and technologies that these companies possess, but do not fully utilize. Such behaviour of the companies can be explained by the absence of active creation and updating of business strategy. The economic evaluation of the innovative process (BTAS) proved that the very implementation of innovations did not lead to a major increase in the profit margin. The situation was different when evaluating the benefits of the digitization process, which brought an increase in sales and corporate margins. A completely new finding has been demonstrated, i.e., if a company has unused equipment which brings opportunity costs as well, it is possible to create space for innovation by removing it, and at the same time the sale of equipment can be a significant financial contributor to innovation.