The conversion of hydrocarbons to produce high-quality diesel fuel can be catalysed by bifunctional materials that contain a metal site and an acid site; it has been assumed that these sites should be as close as possible in order to enhance catalysis, but it is now shown that having them too close together can be detrimental to selectivity. New generations of monofunctional catalysts increasingly benefit from precisely controlled and optimized nanoscale features. Jovana Zečević et al. now show that optimization at the nanoscale can also improve the performance of the bifunctional hydrocracking catalysts widely used for the production of high-quality diesel fuels. These catalysts contain a metal site and an acid site, and for many years the received wisdom was that these sites should be as close as possible for optimum performance. But Zečević et al. find that having them too close together can be detrimental to selectivity, and that the sites should be positioned at nanometre-scale separations. This work may lead to more effective diesel production from alternative sources such as natural gas, vegetable oil and algal oil. The ability to control nanoscale features precisely is increasingly being exploited to develop and improve monofunctional catalysts1,2,3,4. Striking effects might also be expected in the case of bifunctional catalysts, which are important in the hydrocracking of fossil and renewable hydrocarbon sources to provide high-quality diesel fuel5,6,7. Such bifunctional hydrocracking catalysts contain metal sites and acid sites, and for more than 50 years the so-called intimacy criterion8 has dictated the maximum distance between the two types of site, beyond which catalytic activity decreases. A lack of synthesis and material-characterization methods with nanometre precision has long prevented in-depth exploration of the intimacy criterion, which has often been interpreted simply as ‘the closer the better’ for positioning metal and acid sites8,9,10,11. Here we show for a bifunctional catalyst—comprising an intimate mixture of zeolite Y and alumina binder, and with platinum metal controllably deposited on either the zeolite or the binder—that closest proximity between metal and zeolite acid sites can be detrimental. Specifically, the selectivity when cracking large hydrocarbon feedstock molecules for high-quality diesel production is optimized with the catalyst that contains platinum on the binder, that is, with a nanoscale rather than closest intimacy of the metal and acid sites. Thus, cracking of the large and complex hydrocarbon molecules that are typically derived from alternative sources, such as gas-to-liquid technology, vegetable oil or algal oil6,7, should benefit especially from bifunctional catalysts that avoid locating platinum on the zeolite (the traditionally assumed optimal location). More generally, we anticipate that the ability demonstrated here to spatially organize different active sites at the nanoscale will benefit the further development and optimization of the emerging generation of multifunctional catalysts12,13,14,15.