Abstract Aims Future phosphorus (P) fertilizer availability faces challenges due to limited phosphate rock mines and strict quality regulations regarding Cd contents in phosphate rock. In this study, conventional fertilization was partially substituted with meat bone meal (MBM), sludge (S), and the organo-mineral combination of S plus MBM (SMBM), in a wheat agroecosystem. Methods We investigated the impact of fertilization treatments and crop phenological stages on P availability, crop yield, and soil microbial responses. Analysis included enzyme activities, microbial biomass, and the composition of bacterial and fungal communities using metabarcoding. Additionally, we estimated functional genes related to the P cycle through qPCR. Crop yield and nutrient content in plants and soil were also determined. Results Replacing traditional fertilization with MBM and SMBM maintained crop yield at levels equivalent to conventional fertilization. S and SMBM produced 70% and 40% (respectively) more bioavailable P compared to conventional treatment (Trad). Significant differences between treatments in soil microbial biomass were observed in the flag leaf stage. S increased in 20% total soil microbial biomass compared to Trad. Crop phenology had a stronger impact on bacterial and fungal communities than fertilization treatments. The use of S enhanced microbial biomass and activity. Yield in both MBM and SMBM plots exhibited no statistically significant differences compared to traditional fertilization. Conclusion Organo-mineral fertilization emerges as a sustainable strategy for maintaining crop production while improving soil functionality. Our findings emphasize the primary influence of crop phenology on shaping soil microbial communities and influencing microbial biomass and functionality.