Bioscientists such as geneticists and molecular biologists regularly demonstrate the integration of domain concepts and science inquiry practices/skills while explaining a natural phenomenon. The complexity of these concepts and skills becomes manifold at the tertiary undergraduate level and are known to be challenging for learners. They learn these in silos as part of theory classes, practical labs, and tutorial sessions while in an industry, they will be required to integrate and apply in a given authentic context. To support learners in this process, we have designed and developed Geneticus Investigatio (GI), a technology-enhanced learning (TEL) environment for scaffolding complex learning in the context of Mendelian genetics. GI facilitates this complex learning by the integration of domain concepts and science inquiry practices through inquiry-driven reflective learning experiences, which are interspersed with inquiry-based learning steps in an authentic context along with metacognitive reflection. In this paper, we present two cycles of iterative design, development, and evaluation of GI, based on the design-based research (DBR) approach. In the first DBR cycle, we identified the pedagogical design features and learning activities of GI based on an exploratory study with bio-science instructors for facilitating complex learning. We then report a pre-post classroom study (N = 37) in which we investigated the learning and perceptions of usability and usefulness of GI. The results indicate high learning gains after interacting with GI and learner perceptions that activities in GI help learn concepts and inquiry practices along with its integration. It is followed by the identification of interaction and other difficulties by the learner, which were triangulated with different data sources. It provided insights into the pedagogical and design changes required in GI. The revised version of GI was evaluated with a quasi-experimental classroom study (N = 121). The results indicate that the drawbacks of the previous version of GI were addressed. The main contributions of this research are a pedagogical design for facilitating complex learning and its implementation in the form of GI TEL environment.