•The aim of the study was to quantify the relationships between innovation activity and the outcomes of e-commerce.•Globalisation processes are accompanied by the dynamic use of information and communication technologies (ICT), which has prompted changes in global economic activities.•We find that the B2C outcomes compared to the B2G outcomes are not fundamentally different, even though lower central tendency outputs were recorded rather in B2G than in B2C.•There was no significant difference between the individual years in the macroeconomic outputs (GDP, global Innovation Index (GII), Human Development Index (HDI). This study quantifies the relationships between innovation activity and the outcomes of business-to-consumer (B2C), business-to-business (B2B), and business-to-government (B2G) e-commerce by companies and the economic development of EU member countries. The relationship of e-commerce with innovation activities and the economic development of countries was evaluated. The analysis input was represented by annual data from the EU from 2013 to 2021, and the indicators of the e-commerce companies (where B2C, B2B, and B2G represent one variable) were classified according to company size. Twelve e-commerce indicators were analyzed in total. The panel regression analysis confirmed that a higher rate of innovation is associated with a higher rate of e-commerce, which, in turn, is associated with a higher rate of economic development in countries. Most of the relationships explored were confirmed. Nevertheless, when specifying them, it is necessary to consider the specifics of B2C and B2B with B2G. The the cluster analysis demonstrated that Bulgaria and Romania are among the countries that should pay more attention to this issue.