Preparing catalysts with highly dispersed metal nanoparticles and narrow particle size distribution has been in the focus of numerous studies. Besides size and size distribution, the location of metal nanoparticles within and local metal loading of the support can have significant impact on catalytic performance. This study revealed that great variations in Pt loading between individual Pt/zeolite Y crystals occurred irrespective of the metal deposition method, namely ion‐exchange (IE) or incipient wetness impregnation (IWI). The variation in Pt loading was found to be directly related to different Si/Al ratios of individual zeolite crystals. Results indicate that this Si/Al variation was likely induced by post‐synthesis treatments, commonly performed to introduce mesoporosity. In view of the great importance of zeolite‐based catalysts for oil refining, understanding the origin of such metal loading heterogeneities may lead to further improvement of zeolite‐based catalytic performance.