Spatio-temporal regulation of protein glycosylation is critical for normal development and is altered in various human pathologies. However, the signaling pathways that confer tissue and cell specific glycan expression patterns are largely unknown. We previously characterized a Drosophila mutation which we named sugar-free frosting (sff), that impacts the expression of a subset of N-linked glycans known as HRP-epitopes in the embryonic nervous system. The gene affected in the sff mutant is the Drosophila homologue of the C.elegans and mammalian SAD kinases. In Drosophila, we demonstrated that the sff mutation affects glycan processing through reorganization of Golgi compartments. However, the downstream effectors through which Sff kinase acts to bring about these changes are currently unknown. To identify the molecular targets of Sff kinase, we undertook differential phosphoproteomic analysis of wildtype and sff mutant embryos collected at the developmental stages at which HRP epitopes first appear. Using immunohistochemistry, genetic analysis, and confocal microscopy, Bifocal (Bif), Rasputin (Rin), and Liprin-alpha (Lip-α) were identified as downstream effectors of Sff signaling in the regulation of glycan processing. In combination with bif or liprin-a mutations, sff double mutants exhibit altered overlap between the trans-Golgi network and cis-Golgi compartment. We also detected Rasputin co-localization with Golgi compartmental markers and this association was altered in sff mutant embryos. Taken together, Bif as a putative cytoskeletal regulator, Lip- α as a coiled coil protein, and Rin as the ortholog of RasGAP SH3 binding protein, highlight downstream pathways through which Sff kinase activity fine tunes protein glycosylation in response to external stimuli.