High-external input agriculture is one of the most disruptive human activities, which have been justified by the current economic paradigm due to high productivity and the need to feed a growing population. However, we are dangerously close to the edge of the planet resources and both hunger and food insecurity has increased. Limiting the use of non-renewable chemical fertilizers and pesticides, changing water management, enhancing diversity and considering the often-neglected social dimension of agriculture are the bases to other chemical and biological technologies to agriculture. Biological inputs can stimulate the substitution of chemical inputs without questioning the current fundaments or can be adopted as a turning point to intensify the harsh processes of transition to more environmental friendly agriculture. The debate is open and our contribution is to develop the scientific basis for biological inputs that, unlike soluble fertilizers and pesticides, depend on a number of factors for its success in promoting crop yield. In this review, we showed the results obtained with the combined use of diazotrophic endophytic bacteria and humic substances in diverse crops (sugarcane, maize, tomato, common beans and pineapple), presenting the main morphological and physiological changes induced by biological technology. A snapshot of the state of the art of the use of plant growth promoting bacteria together with humic substances was provided, showing their potential especially when plants are subjected to moderate to severe abiotic stress. The number of studies reporting the combined use of plant growth promoting bacteria and humic substances is surprisingly low. There is an open avenue for research and encouraging debate is the goal. To overcome the conventional agriculture, maintaining productivity levels is more than scientific challenge, is a humanitarian duty. The biological inputs can help in this purpose.