Background/Objectives: The melt-spinning process has seen limited application in the pharmaceutical industry. However, nano- and microfibrous structures show significant potential for novel drug delivery systems, due to their high specific surface area. To facilitate broader adoption in pharmaceutical technology, critical parameters influencing fiber quality and yield must be investigated. In this study, we aimed to develop an isomalt-based microfibrous carrier system for active pharmaceutical ingredients. Methods: The effects of different isomalt compositions—specifically, varying ratios of GPS (6-O-α-d-glucopyranosyl-d-sorbitol) and GPM (1-O-α-d-glucopyranosyl-d-mannitol)—as well as key process parameters, were systematically investigated to optimize fiber formation. The prepared fibers underwent different treatments. Morphological changes were monitored with a microscope, and microstructural changes were studied using a differential scanning calorimeter and X-ray diffractometer. The macroscopic behavior of the fibers was evaluated by image analysis under monitored conditions. Results: Statistical analysis was used to determine the optimal setting to produce isomalt-based fibers. We found that storage over ethanol vapor has a positive effect on the stability of the fibers. We successfully prepared ibuprofen sodium-containing fibers that remained stable after alcohol treatment and enabled drug release within 15 s. Conclusions: It was found that the applied GPS:GPM isomalt ratio significantly influenced fiber formation and that storage over ethanol positively influenced the processability and stability of the fibrous structure. An isomalt-based microfibrous system with advantageous physicochemical and structural properties was successfully developed as a potential drug carrier. The system is also resistant to the destructive effects of ambient humidity, enabling preparation of suitable dosage forms.