Biomedical applications of polymers require precise control of the solid-state structure, which is of particular interest for biodegradable copolymers. In this work, we evaluated the influence of crystallization conditions on the comonomer exclusion/inclusion balance of biodegradable poly(butylene succinate-ran-butylene adipate) (PBSA) isodimorphic random copolymers. Regardless of the crystallization conditions, the copolymers retain their isodimorphic character, displaying a pseudo-eutectic behavior with crystallization in the entire composition range. This illustrates the thermodynamic nature of the isodimorphic behavior for PBSA random copolymers. However, depending on the composition, the crystallization conditions affect the exclusion/inclusion balance of the comonomers. Fast cooling favors butylene adipate (BA) inclusion inside the poly(butylene succinate) (PBS) crystals, whereas isothermal crystallization strongly limits it. PBA-rich compositions behave differently. Both fast and slow crystallization formed the β-phase, whereas BS unit inclusion is favored independently of the cooling conditions. During successive self-nucleation and annealing, the BA inclusion is intermediate between non-isothermal and isothermal conditions, while the crystalline structure of the PBA phase changes from the β-phase to the more stable α-phase. We propose a simple crystallographic model to explain the changes in the unit cell dimension of the copolymers.