In order to overcome the exploration–exploitation paradox, structural ambidexterity literature suggests establishing differentiated units for exploitation and exploration with a carefully managed exploration–exploitation interface supporting cross‐fertilization without cross‐contamination. Recent research demonstrates the crucial role of integration mechanisms (i.e. how knowledge exchange between exploratory and exploitative units can be organized) and related transition modes (i.e. how exploratory innovations can ultimately be transferred back into the exploitative structures of core business) to deal with this challenge. However, a systematic account of the diverse tensions, risks, and trade‐offs associated with integration which may ultimately cause exploration failure is missing, so far. This paper presents a longitudinal process study uncovering the anatomy of an unsuccessful exploration of (green) technologies by a medium‐sized entrepreneurial firm. We investigated their transition processes to understand how the managers dynamically configured and reconfigured the exploration–exploitation interface over time. Our theoretical contribution lies in providing a framework of six integration trade‐offs (Exploratory‐complementary linking vs. contamination; Seeking legitimacy early on vs. frustration at discontinuation of innovation; Boundary spanning through job rotation vs. carrying over of old culture; Early vs. premature transfer; Reorganization vs. capability mutation; and Improved access to core business resources vs. resource starvation) linked to three phases in the transition process (before, at, and after transfer). We also highlight mechanism, pulling‐forward, and streamlining‐related failures linked to integration trade‐offs in resource‐constrained contexts. Our implication for R&D and top management is that the use of integration mechanisms for structural ambidexterity bears the risk of cross‐contamination between the exploitative and exploratory structures and are therefore inevitably linked to trade‐offs. To minimize negative side effects and prevent exploration failure, organizations have to consciously select, schedule, operationalize, and manage (re)integration mechanisms along the transition process. Our framework of integration trade‐offs systematically supports managers in their organizational design choices for integration mechanisms in the transition processes.