One of the best methods for producing bulk homogeneous (composition) supported bimetallic AuPd clusters involves the immobilization of a protected Au seed followed by the addition of Pd. This paper investigates the importance of this gold seed in controlling the resulting bimetallic AuPd clusters structures, sizes and catalytic activities by investigating three different gold seeds. Uniform Au-Pd alloy were obtained when a steric/electrostatic protecting group, poly(vinyl alcohol) (PVA), was used to form the gold clusters on activated carbon (AC). In contrast Au/AC precursors prepared using Au nanoparticles with only electrostatic stabilization (tetrakis(hydroxypropyl)phosphonium chloride (THPC)), or no stabilization (magnetron sputtering) produced inhomogeneous alloys and segregation of the gold and palladium. The uniform alloyed catalyst (Pd@Au(PVA)/AC) is the most active and selective catalyst, while the inhomogenous catalysts are less active and selective. Further study of the PVA protected Au clusters revealed that the amount of PVA used is also critical for the preparation of uniform alloyed catalyst, their stability, and their catalytic activity.