Crystallization represents a fundamental process engendering solidification of a material and determines its microstructure. Driven by complex phenomena at the atomic scale, its understanding for alloys still remains elusive. The present work proposes a large scale molecular dynamics simulation study of the homogeneous crystal nucleation pathways of prototypical undercooled Al-Ni binary alloys. An unsupervised topological learning analysis shows that the nucleation sets in first from a chemical ordering, followed by a bond-orientational ordering of the underlying crystal phase. Our results indicate also a different polymorph selection that depends on composition. While the nucleation pathway of Al50 Ni50 displays a single step with the emergence of B2 short-range order, a step-wise nucleation toward the L12 phase is seen for Al25 Ni75 . The influence of the nucleation of pure Al and Ni counterparts is further discussed.