Relativistic jets launched by active galactic nuclei are fundamental for understanding the physics of accreting supermassive black holes and their immediate environment, but the mechanisms that drive the jet launching remain uncertain. We investigate the sub-parsec jet of 3C 84 using multi-epoch multi-frequency very long baseline interferometry (VLBI) observations with the European VLBI Network and the Very Long Baseline Array at 22 and 43GHz. We analysed the evolution of the spectral index gradient in the core region to relate the observed structure to physical interpretations and to distinguish between competing jet-launching models. Furthermore, we examined the effect of the ambient medium and magnetic field configuration on the jet morphology and dynamics over time and explored their connection to a coinciding gamma-ray flare. Our spectral analysis reveals significant changes across three epochs, indicating dynamic activity between filamentary structures on sub-parsec scales, evolving magnetic fields, and a complex interaction with the surrounding medium, all of which shape the innermost jet and might affect its high-energy emission.