Organic nanofertilizers are derived from the innovative bio-inputs Compost Altoandino and AOLA, which are relevant to agricultural production. Their potential for bioremediation of contaminated agricultural soils was studied. The effectiveness of these bio-inputs in bioremediating agricultural soils contaminated by hydrocarbon derivatives—dielectric oil, used automotive oil, gasoline, diesel, and kerosene—was evaluated by their effects on physicochemical, biological, and organoleptic soil variables, as well as on the qualities of indicator plants. Favorable responses were found in both the soil and the plant, and a direct relationship was discovered between bioremediation and microbial metabolism. Innovative bio-inputs possess a unique microbiota, comprised of complex communities of fungi, bacteria, actinomycetes, viruses, microfauna, and other organisms. Under natural conditions, these organisms are potent and resilient, with a multifaceted and versatile capacity to degrade contaminating hydrocarbon molecules through their metabolism and the production of specific substances such as enzymes, vitamins, hormones, proteins, antibiotics, and other as-yet-unknown organic compounds. This process enables the remediation of contaminated soils and promotes normal plant growth. Due to their effectiveness and bioremediation capacity, regardless of the contaminant type, treatments the high-Andean compost combined with AOLA (Aerobic liquid organic fertilizer), proved to be the most effective for bioremediating contaminated soils and promoting plant growth and development, thanks to their excellent biological complementarity.