Soil quality is declining in Europe and globally due to agricultural practices and climate change. The European market for novel biobased fertilisers (BBFs) is growing and the new European Union fertiliser regulation promotes their use. However, knowledge about the effects of many novel BBFs on soil quality is currently very limited. In a one-year laboratory incubation experiment, this study aimed to test the effect on biological (microbial biomass carbon (C)), physical (clay dispersibility and water-holding capacity) and chemical (pH, cation exchange capacity (CEC), total C and C in soil size fractions (<250, 50–250 and >50 μm)) soil quality indicators of 10 BBFs applied at two different rates on two soil types: an Arenosol and a Luvisol. The set-up also included a soil that was subjected to long-term annual application of the compost used in the incubation. The application of BBFs generally improved soil quality, with the compost material improving soil quality most, followed by a plant-based fertiliser and a biogas digestate. The effect of BBF application on CEC, total C and particulate organic matter (POM) was related to the amount of total C added with the BBF. Furthermore, the effect on total C and POM fractions was also related to easily decomposable C added with the BBF. Comparing the single accelerated application with annual application under field conditions indicated that the long-term incubation trial is a reasonable predictor of compost long-term effects in the field. Whether this applies to BBFs with very different properties remains to be shown.