The Circular Economy concept implies the re-design of existing production systems in agriculture, by promoting agricultural waste recycling. In an organic zucchini-lettuce rotation, two different agroecological tools were considered: biofertilizer and presence or absence of green manure (GM+ and GM-). In particular, we compared: (i) anaerobic digestate from cattle manure, co-composted with vegetable wastes, with the presence of GM (AD GM+); (ii) olive pomace compost, re-composted, with the presence of GM (OWC GM+); (iii) municipal waste compost with GM (MWC GM+); (iv) municipal waste compost without GM (MWC GM-). These materials were tested with a commercial organic fertilizer without GM (COF GM-) as a positive control. The objectives were: (i) assessing the environmental sustainability of biofertilizers through carbon footprint analysis by greenhouse gas-GHG-emissions; (ii) evaluating the agronomic performance on the vegetable rotation, by energy output assessment. The total carbon emissions of biofertilizers production was 63.9 and 67.0 kg of CO2 eq Mg-1 for AD and OWC, respectively. The co-composting and re-composting processes emitted 31.4 and 8.4 kg CO2 per Mg of compost, respectively. In AD the ventilation phase of composting accounted for 37.2% of total emissions. The total CO2 emission values for the two-crop cycles were the highest in COF GM- and the lowest in OWC GM+, due to different fertilizer sources. On the average of the treatments, the input that induced the highest CO2 emission was irrigation (37.9%). The energy output assessment for zucchini and lettuce highlighted similar performance for all the treatments. Our findings demonstrated the validity of the tested processes to recycle agro-industrial wastes, and the potential of agroecological practices (GM) to mitigate GHG emissions.