This paper presents the possibility of creating motivational programs for employees working in small and medium-sized enterprises (SMEs). The applicability of the proposed option is verified and presented to a medium-sized enterprise operating in the wood-processing industry in Slovakia. Using cluster analysis, three motivational-oriented groups were defined in the category of managers and three similar motivational-oriented groups in the category of workers. Subsequently, the sampling units were tested by the Tukey’s honest significant difference (HSD) test. In this way, the significance of the differences in arithmetic mean and the standard deviation of the individual motivational factors of the monitored sets at the significance level α = 0.05 were defined. The result of the analysis is a plan to create a group motivational program. The content of this program is a common motivational factor for groups, supplemented by employee-specific factors. Currently, businesses apply unified motivational programs based on two, three, or four main motivators. However, improperly designed and applied motivational programs have a negative impact on employees and do not motivate them to maximize performance. By implementing this method in wood-processing SMEs, the company’s performance can be increased, as the needs of most employees would be met.