In this context, our group has dedicated a long lasting and continuous effort in the development of reliable protocols to parameterize quantum-mechanically-derived FFs (QMD-FFs). Despite the original procedures separately addressed the QMD-FF's intra- and inter- molecular terms (which respectively govern the flexibility of each molecule and the interactions among them), a complete parameterization protocol has been also recently reported. Therein, the inter-molecular parameterization was handled by the PICKY procedure, whereas the QMD-FF intra-molecular parameters were obtained following the original JOYCE protocol. Since then, the JOYCE code has been stepwise refined, and, along this development, it has been applied to different topics, ranging from the electronic properties of flexible organic molecules and transition metal complexes (TMCs) with octahedral symmetry, to the nano-scale friction of polymeric chains at metal surfaces. Moreover, its capability of building reliable excited state FFs has recently led to the integration of the JOYCE protocol in multi-level approaches for computational spectroscopy and, more recently, to investigate the photophysics of molecular systems. Most of the aforementioned developments are now consistently implemented in a new version of the code, JOYCE3.0, which constitutes the focus of this work. The whole parameterization procedure has been in fact significantly automated and updated: among the most relevant improvements, we highlight the new interfaces with electronic structure methods and popular MD codes, the automatic generation of the target molecule internal coordinates and the implementation of different routes to consistently tackle highly flexible molecular scaffolds.