Protein glycosylation, a fundamental modification critical for diverse biological functions, is well orchestrated within the Golgi apparatus, a central organelle in the secretory pathway. This review explores the mechanisms by which the Golgi governs protein-specific glycan modification, emphasizing the spatial organization of glycosyltransferases within the Golgi and the regulated transport of glycoproteins through its compartments. Specificity arises from the strategic localization of glycosyltransferases within the Golgi, enabling them to recognize both glycan structures and protein domains on their substrates. Advanced imaging reveals a complex and dynamic organization within the Golgi, challenging traditional models and highlighting specialized zones. Regulated transport of glycoproteins through the Golgi is critical for controlling their access to modifying enzymes. Specific sequence motifs within glycoproteins can act as ‘passport sequence’, directing them to distinct Golgi regions and influencing glycosylation by altering their proximity to specific enzymes and accessory proteins. These mechanisms support the hypothesis that sequence-dependent signals within substrate proteins influence their trafficking, enabling precise glycosylation as they transit the Golgi. Understanding these processes provides new insights into how glycan diversity is generated and regulated within the Golgi, highlighting the interplay between enzyme localization, protein trafficking, and the dynamic organization of this essential organelle.