More than 20% of global carbon emissions are linked with the production of construction materials used in the built environment. The use of bio-materials along with urban densification strategies that avoid demolition and reduce material demand, have been recommended to achieve urban sustainability goals. Addressing these measures, this study compares the life cycle embodied carbon emissions of seven hybrid top-up structural systems composed of concrete, steel and advanced engineered timber products made out of softwood and hardwood species. The life cycle carbon emissions (expressed in kgCO2-eq) were estimated following a cradle-to-grave approach, with a functional unit equivalent to 1 m2 of top-up structural system and focusing on The Netherlands and the city of Amsterdam as main geographical scope. A statistical analysis was included to account for the potential variation of emissions across each life cycle stage, using Monte Carlo simulations for random sampling. The results indicate that predominantly bio-based structures present a staggering 60% lower embodied carbon emissions compared with predominantly concrete, steel and modestly hybrid systems. Preserving the long-term carbon storage capacity of timber elements through high-quality reuse can offset 30–60% of the total positive emissions of the predominantly bio-based systems. Up to 6MtCO2-eq of the national carbon budget in The Netherlands can be saved from a radical uptake of bio-based structures in Amsterdam by 2050. Diversification of material diets with bio-based alternatives is recommended, along with established policy that can guarantee sustainable sourcing and prolonged lifespans through high-end reuse practices.