Extrusion bioprinting is considered promising in cartilage tissue engineering since it allows the fabrication of complex, customized, and living constructs potentially suitable for clinical applications. However, clinical translation is often complicated by the variability and unknown/unsolved issues related to this technology. The aim of this study was to perform a risk analysis on a research process, consisting in the bioprinting of a stem cell-laden collagen bioink to fabricate constructs with cartilage-like properties. The method utilized was the Failure Mode and Effect Analysis/Failure Mode and Effect Criticality Analysis (FMEA/FMECA) which foresees a mapping of the process to proactively identify related risks and the mitigation actions. This proactive risk analysis allowed the identification of forty-seven possible failure modes, deriving from seventy-one potential causes. Twenty-four failure modes displayed a high-risk level according to the selected evaluation criteria and threshold (RPN > 100). The results highlighted that the main process risks are a relatively low fidelity of the fabricated structures, unsuitable parameters/material properties, the death of encapsulated cells due to the shear stress generated along the nozzle by mechanical extrusion, and possible biological contamination phenomena. The main mitigation actions involved personnel training and the implementation of dedicated procedures, system calibration, printing conditions check, and, most importantly, a thorough knowledge of selected biomaterial and cell properties that could be built either through the provided data/scientific literature or their preliminary assessment through dedicated experimental optimization phase. To conclude, highlighting issues in the early research phase and putting in place all the required actions to mitigate risks will make easier to develop a standardized process to be quickly translated to clinical use.