Recent works on Generalized Referring Expression Segmentation (GRES) struggle with handling complex expressions referring to multiple distinct objects. This is because these methods typically employ an end-to-end foreground-background segmentation and lack a mechanism to explicitly differentiate and associate different object instances to the text query. To this end, we propose InstAlign, a method that incorporates object-level reasoning into the segmentation process. Our model leverages both text and image inputs to extract a set of object-level tokens that capture both the semantic information in the input prompt and the objects within the image. By modeling the text-object alignment via instance-level supervision, each token uniquely represents an object segment in the image, while also aligning with relevant semantic information from the text. Extensive experiments on the gRefCOCO and Ref-ZOM benchmarks demonstrate that our method significantly advances state-of-the-art performance, setting a new standard for precise and flexible GRES.