This work demonstrates the potential of zeolite Y supported nickel phosphide materials as highly active catalysts for the upgrading of bio-oil as an improved alternative to noble metal and transition metal sulphide systems. Our systematic work studied the effect of using different counterions (NH4+, H+, K+ and Na+) and Si/Al ratios (2.56 and 15) of the zeolite Y. It demonstrates that whilst the zeolite counterion itself has little impact on the catalytic activity of the bare Y-zeolite, it has a strong influence on the activity of the resulting nickel phosphide catalysts. This effect is related to the nature of the nickel phases formed during the synthesis process Zeolites containing K+ and Na+ favour the formation of a mixed Ni12P5/Ni2P phase, H+ Y produces both Ni2P and metallic Ni, whereas NH4+ Y produces pure Ni2P, which can be attributed to the strength of the phosphorus-aluminium interaction and the metal reduction temperature. Using quinoline as a model for the nitrogen-containing compounds in bio-oils, it is shown that the hydrodenitrogenation activity increases in the order Ni2P > Ni0 > Ni12P5. While significant research has been dedicated to the development of bio-oils produced by thermal liquefaction of biomass, surprisingly little work has been conducted on the subsequent catalytic upgrading of these oils to reduce their heteroatom content and enable processing in conventional petrochemical refineries. This work provides important insights for the design and deployment of novel active transition metal catalysts to enable the incorporation of bio-oils into refineries.