The production of mineral fertilisers relies heavily on mineral deposits that are becoming depleted or is based on processes that are highly energy demanding. In this context, and in line with the circular economy and the European Green Deal, the recovery of nitrogen (N), phosphorus (P), and potassium (K) from organic wastes using chemical technologies is an important strategy to produce secondary raw materials for incorporation into mineral fertilisers, partially replacing the traditional sources of N, P, and K. However, there are very few studies on the agronomic and environmental effects of such substitution. The aim of this work was to evaluate plant growth under microcosm conditions and the effect on the soil microbiome of mineral fertilisers in which part of the N, P, or K content comes from bio-based materials (BBMFs), namely ash, struvite, and a patented chemical process. The crop was maize, and a metataxonomic approach was used to assess the effect on the soil microbiome. The BBMF treatments were compared with a control treated with a conventional mineral fertiliser. The conventional fertiliser performed significantly better than the bio-based fertilisers in terms of maize biomass production at the first sampling point 60 days after sowing (DAS), but at the last sampling point, 90 DAS, the BBMFs showed comparable or even better biomass production than the conventional one. This suggests that BBMFs may have a slightly slower nutrient release rate. The use of fertiliser, whether conventional or BBMF, resulted in a significant increase in microbiome biodiversity (Shannon index), while it did not affect species richness. Interestingly, the use of fertilisers modulated the composition of the bacterial community, increasing the abundance of beneficial bacterial taxa considered to be plant-growth-promoting bacteria, without significant differences between the conventional mineral fertilisers and the BBMFs. The predominance of PGPRs in the rhizosphere of crops when BBMFs are used could be part of the reason why BBMFs perform similarly or even better than conventional fertilisers, even if the rate of nutrient release is slower. This hypothesis will be tested in future field trials. Thus, BBMFs are an interesting option to make the food chain more sustainable.