Over the years, the practice of agriculture has transformed from the era of traditional to that of intensive agriculture in the bid to boost the production index that will satisfy the food needs of the globally growing population. However, the continuous and exaggerated use of chemical fertilizers and pesticides has resulted in major adverse impacts on food and environmental safety, whereas most traditional techniques for reclamation of natural soil nutrients, including shifting cultivation and polyculture, are no longer attractive measures of land rejuvenation. There is, therefore, the need for urgent evaluation and adoption of innovative methods of replenishing the agricultural soils that conform to the current agricultural systems without exerting undesirable effects on the ecosystem. In this review, we elucidated the use of key bioresources, such as organic fertilizers, biofertilizers, and biopesticides, as alternatives to chemical-based products in attaining a safe and sustainable agricultural system. Bioresources are naturally available, safe, and easily accessible products. The potential of these biological products in fostering soil microbial growth, plants’ productivity, and induced host immunity to diseases, alongside the promotion of healthy soil–microbe–plant relationships and preservation of the ecosystem processes without disruption, are aspects that were also explored. Therefore, the productive use of bioresources is considered strategic as it pertains to attaining safe and sustainable food production.

Soil fertility decline and yield variability remain the major challenges for smallholder farmers in sub-Saharan Africa. Yet the influence of socioeconomic and agronomic drivers is not fully understood. This study evaluated the effects of gender, education level, fertilizer use, and cultivation duration on soil fertility and soybean–maize rotation yields in Rwanda. A survey of 384 farmers was conducted in Nyagatare and Huye districts using a semi-structured questionnaire and field-based soil assessments. In Nyagatare, 67.7% of farmers use of both N and P fertilizers, while 66.7% use farmyard manure (FYM). The adoption of FYM use was significantly associated with male farmers (Χ² = 22.7, p < 0.001). In Huye, adoption of mineral fertilizer was low (35.5% for N, and 37.5% for phosphorus “P”), while 74% of farmers use FYM. Moreover, male farmers exhibited significant associations with the use of P fertilizers (Χ² = 6.1, p = 0.01), and FYM (Χ² = 14.2, p < 0.001). Fields that received FYM exhibited greater soil pH with 0.2 ± 0.1 units, soil OC (+ 0.2%, p = 0.01). Fields cultivated for 10 years presented significantly higher CEC (+ 0.5 cmol_c kg⁻¹, p = 0.02). These results demonstrated that farmers’ socio-economic characteristics and fertilizer management practices are closely associated with soil properties and crop yields in Nyagatare and Huye districts. Future research should extend to the field experiments to validate these relationships and optimize the development of evidence-based soil fertility management strategies.