To evaluate the agronomic value of animal manure, we quantified the effects of pedo-climatic, crop and management factors on crop productivity, N use efficiency, and soil organic matter, described with simple indicators that compare manures with mineral fertilizers. We selected 80 European long-term field experiments that used bovine farmyard manure or bovine liquid slurry, alone (FYM and SLU) or combined with mineral fertilizers (FYMm and SLUm), and compared them to mineral fertilizer only reference treatments. We collected 5570 measurements from 107 papers. FYM produced slightly lower crop yields (−9.5%) when used alone and higher (+11.3%) yields when used in combination with N fertilizer (FYMm), compared to those obtained using mineral fertilizers only. Conditions promoting manure-N mineralization (lighter soil texture, warmer temperature, longer growing season, and shallower incorporation depth) significantly increased the effect of FYM/FYMm on crop yield and yield N. The production efficiency of FYM (yield:N applied ratio) was slightly lower than that of mineral fertilizers (-1.6%). The apparent N recoveries of FYM and FYMm were 59.3% and 78.7%, respectively, of mineral fertilizers. Manured soils had significantly higher C (+32.9% on average for FYM and FYMm) and N (+21.5%) concentrations. Compared to mineral fertilizers, yield was reduced by 9.1% with SLU, but not with SLUm. Influencing factors were similar to those of FYM/FYMm. Efficiency indicators indicated SLU (but not SLUm) was less effective than mineral fertilizers. Slurry significantly increased SOC (on average for SLU and SLUm by +17.4%) and soil N (+15.7%) concentrations. In conclusion, compared to mineral N fertilizers, bovine farmyard manure and slurry were slightly less effective on the crop, but determined marked increases to SOC and soil N, and thus, to long-term soil fertility maintenance.