Excessive chemical fertilizers harm the environment, economy, and health, while compost and its extracts provide a sustainable solution. Consequently, the development of liquid organic amendments with biofertilizing and antioxidant capabilities is of significant interest in intensive agriculture. To achieve this, four Compost Extraction Protocols (CEP1–4) were applied to different compost to obtain a range of aqueous extracts. These treatments varied in temperature, incubation duration, and agitation. The raw materials for the compost used were Agri-food Waste (AW), Sewage Sludge (SS), Vegetable Waste (VW), and Olive Mill Waste (OMW). The extracts were characterized in physicochemical terms and their potential to promote radicle germination in cucumber and lettuce seeds. Additionally, counts of microbial groups associated with biofertilizing capacity were conducted. Three extracts were chosen based on the germination index to conduct an in vivo bioassay on seedlings. Finally, oxidative stress in radicles and seedlings resulting from the preceding tests was evaluated by quantifying malondialdehyde (MDA), total phenolic compounds (TPC), and ascorbate-glutathione cycle enzymes. The results established that protocols with milder temperatures, such as CEP1 and CEP4, yielded aqueous compost extracts with good biofertilizing and antioxidant properties, although the effect was dependent on crop sensitivity. Specifically, the extracts selected for the seedling trial, OMW-A CEP4, AW-A CEP1, and especially AW-A CEP4, demonstrated a remarkable biofertilizing and antioxidant properties in lettuce, by increasing growth parameters and TPC while decreasing MDA. The results indicate that aqueous compost extracts are a suitable alternative to reduce the consumption of chemical fertilizers.