The swift adoption of digitalization and transformation within enterprises and their operations had commenced prior to the onset of COVID-19, characterized by the shift towards Industry 4.0 and subsequently progressing towards Industry 5.0. However, mandated restrictions significantly amplified the necessity and drive to utilize digital tools for both businesses and consumers. New opportunities previously not utilized have arisen yet are hand in hand with several risks linked to the use of these new digital tools. The bioeconomy sector is not an exception. The study aims to consider the sector representatives’ opinions on the significance of the risks related to digitalization. The empirical results of this study stem from a survey of enterprises in the bioeconomy sector carried out in 2020 and 2021 in Latvia. The research results prove that there are many factors influencing the development of digitalization. The results notably affirm that both entrepreneurs and employees in SMEs recognize the considerable importance of these risks, particularly emphasizing the significance of security and technology risks. While the Chi-Square Test of Independence indicates a notable association between risk evaluation scores and the education level of respondents before the COVID-19 outbreak in 2020, this association diminishes in 2021. Contrary to the hypothesis that individuals with higher education levels are more attentive to risks, the evidence shows inconsistency in their perception, particularly regarding professional challenges of the entrepreneur and employees to use digital tools and other risk categories. However, the relationship between higher education levels and the significance of risks pertaining to security risks, technology risks, and the skills of the clients to use digital tools is partly affirmed.