This paper addresses an experimental investigation of the microinjection molding process through three increasing sections of polyoxymethylene (POM) stepped parts. High and low levels of mold temperature and injection velocity were defined to evaluate the relationship between machine settings, melting and crystallization properties, morphology formation, and shrinkage. The internal morphology of parts showed a mix of structures, from the mold surface towards the core region of each section. Differential scanning calorimetry (DSC) tests highlighted the difficulty of concluding the relationship between the melting temperatures, the processing conditions, and the position of the samples within the mold. The skin‐layer crystallinity declines with increasing part‐step thickness, while the crystallinity degrees of intermediate and core layers are sensitive to the thermal gradients. It was also observed that crystallinity rises along with increasing thickness, benefiting from further polymer chain relaxation and perfection. The unsymmetrical mold cavity results in substantial differences in shrinkage. High shrinkage occurs across the thickness direction due to fast material solidification. The experimental results were supported by the calculated shear rates and temperature fields at the end of the mold‐filling phase. This work yields new insights into comprehending the intricate flow and thermal properties of stepped micropart geometries, which are widely encountered in the plastics manufacturing industry.