The European Go-Lab project aims to promote Inquiry-based Learning (IBL) with online laboratories. To support teachers and students in this endeavor, the project provides an IBL model (a sequence of inquiry phases) as well as the technological infrastructure to implement it: the Graasp platform and the Golabz repository. Using these technologies, teachers create Inquiry Learning Spaces (ILSs) where they adapt the proposed IBL model to their needs, and enrich each one of its phases with online resources, apps or labs to build a web-based learning environment and distribute it to the students. The aim of this paper is to reflect on the deviations from the model proposed within the project on the teacher model and the way students adapt it. For that purpose, we analyzed the 102 most frequently used ILSs with respect to the perspectives of teachers and students. The results show deviations of the authored spaces from the pedagogical model of inquiry learning as well as deviations in the actual learning process models from the teachers’ specifications. Additionally, the analysis points out best practices for the learning design, particularly the inclusion of resources and apps into the spaces.