Nutrient use efficiency (NUE), as one of the agriculture ecological efficiency measures, is an important concept to evaluate the production systems of the crop. NUE in organic farming is less studied. Large quantities of poultry manure are needed in organic farming, therefore biological fertilizer is considered to increase the efficiency of fertilizer use. The research was aimed at investigating the effects of poultry manure rates and biofertilizer on edamame yield and the NUE from two experiments at different times. The experiments were done in 2023 and 2024. Each experiment was arranged in a split plot block design with biofertilizer as the main plot (without and with) and poultry manure rates as subplot (0, 8, 16, and 24 tonnes ha-1), replicated 3 times. A combined analysis of variance from two experiments was done. The study investigated the edamame pod yield, agronomic efficiency based on manure rates and based on N, P, K supplied by manure (AE, AEN, AEP, AEK), and partial factor productivity (PFPN, PFPP, PFPK). The results revealed that filled pod number and weight of aboveground biomass increased with higher manure rates. The effect of interaction between biofertilizer, manure rates, and year was significant on pod weight per plant and edamame pod yield. The increases in pod weight and pod yield following manure rates showed different trends according to the presence or absence of biofertilizer and differences in experimental time. Higher increases in pod weight (141.5-293.3%) and pod yield (125.5-174%), following manure rates, occurred in the first trial with biofertilizer. In Experiment 2, pod yield was not affected by manure rates either with or without biofertilizer. AE, AEN, AEP, and AEK were significantly affected by the interaction of biofertilizer, manure rates, and year of the experiment; they decreased with increasing manure rates in the first experiment. Positive values of AE, AEN, AEP, and AEK were found in the first experiment with biofertilizer. In contrast, in the 2nd experiment, positive values of AE, AEN, AEP, and AEK were found without biofertilizer. PFPN, PFPP, and PFPK decreased with higher poultry manure rates. Different soil characteristics and methods of biofertilizer application between two experiments may affect the NUE