Land degradation and the effects of climate change are increasing arid lands, accelerating desertification, and leading to the loss of ecosystem services worldwide. This research focused on evaluating how human impact and environmental factors affect the development of Solanum peruvianum in its natural habitat of coastal lomas. The study was carried out in the coastal lomas of Mangomarca-Peru, where phenotypic and ecological data on the plants were collected. Information was also gathered on human impacts on the nutritional characteristics of the soils. Then, five types of organic amendments were used to improve the physical and chemical characteristics of the degraded soil, and the development and photosynthetic activity of S. peruvianum were evaluated. As a result, under the study conditions, it was found that S. peruvianum was established approximately 33.74 cm from the rocks, in a range of 300 to 650 m asl. The maximum height of the plants was 90 cm, with a stem diameter at ground level of 2 cm. S. peruvianum produced fruits between January and July, with a seed germination rate of 36% in 25 days. On the other hand, the anthropogenic impact on the soil reduced 58% of organic material (OM), 71% of nitrogen, 40% of P2O5, and 13% of K2O and increased the concentration of magnesium oxide, calcium oxide, pH, and electric conductivity (EC). The organic amendments bokashi, compost, and biochar, when mixed with the degraded soil, increased the pH, OM, N, P, and EC; however, the plants died after 25 days. On the other hand, the application of the Premix5 substrate for 100 days favored the growth of 52.84 cm and 38.29 cm in the preserved soil and 23.21 cm in the black soil mixed with blond peat, and it should be noted that the substrates presented an acid pH and EC > 0.1. Regarding photosynthetic phenotyping, S. peruvianum plants grown in their natural habitat and in Premix5 showed a higher proton flux (vH+), linear electron flow (LEF), and maximum quantum yield (Fv’/Fm’). On the contrary, they showed a lower NPQt value than plants grown in preserved and black soil mixed with blond peat.