In this work we investigate the complex processes of Fused Deposition Modelling (FDM) of Polylactic acid (PLA) through a comprehensive model based on the phase-field method. The work studies the immediate post-extrusion flow dynamics of the filament, its temperature evolution, crystallization behaviour and the development of residual stresses and strains. Subsequently, mechanical loading simulations are conducted to determine the effective elastic modulus. The simulation studies were done using an automated workflow implemented in the research data and management framework Kadi4Mat [1], which allows for easier and effective management of the simulations data and their metadata. The studies offer insights into the influence of process parameters, particularly temperature and viscosity, on the filament’s morphology, which in turn affect the mechanical properties of the final structure. The core findings indicate that elevated temperatures and reduced viscosity lead to significant morphological changes, such as filament flattening and alterations in pore shapes within the printed structure. These changes are pivotal as they affect the effective elastic modulus due to the pores being non-load bearing elements which weakens the whole structure. The study also shows that crystallinity of PLA is suppressed due to high cooling rates. In conclusion, this contribution presents a versatile simulation workflow that adapts to various materials and process conditions, and provides a basis for a more nuanced investigation of the processes of FDM on a mesoscopic scale [2].