The Kar9 pathway promotes nuclear fusion during mating and spindle alignment during metaphase in budding yeast. How Kar9 supports the different outcome of these two divergent processes is an open question. Here we show that three sites in the C-Terminal disordered domain of Kar9 mediate tight Kar9 interaction with the C-Terminal dimerization domain of Bim1 (EB1 orthologue). Site1 and Site2 contain SxIP motifs; however, Site3 defines a novel type of EB1-binding site. Whereas Site2 and Site3 mediate Kar9 recruitment to microtubule tips, nuclear movement, and karyogamy, only Site2 functions in spindle positioning during metaphase. Site1 in turn plays an inhibitory role during mating. Additionally, the Kar9- Bim1 complex is involved in microtubule-independent activities during mating. Together our data reveal how multiple and partially redundant EB1-binding sites provide a microtubuleassociated protein with the means to modulate its biochemical properties to promote different molecular processes during cell proliferation and differentiation.