The Drosophila scaffolding protein Zasp52 is required to maintain structure at the muscle Z-disc which experiences strong forces during contraction. It is alternatively spliced into many isoforms, some of which contain a long intrinsically disordered region (IDR). We show that this region is primarily expressed in the indirect flight muscle (IFM) and is required for maintaining integrity of the Z-disc. Deleting the IDR-encoding exon15e results in flightlessness and structural IFM defects, including sarcomere bending at the Z-disc and an inability to de-contract. These defects are indicative of a lack of proper thin filament anchoring to the Z-disc. This is further supported by a genetic interaction between exon15e and actin. Fluorescence recovery after photobleaching of an isoform lacking exon15e shows that the IDR is required for maintaining Zasp52 at the Z-disc and thereby stabilizing Z-discs. Lastly, we can rescue these phenotypes by restricting IFM use. Together, these results suggest that Zasp52s IDR confers thin filament stability at the Z-disc of IFM.