Agricultural production activities generate a large amount of waste, most of which is of organic origin from plant remains. These residues could easily be transformed into a resource, specifically, into a substrate for use in soilless cultivation; however, in most cases, they are not used. Therefore, a characterization of local agricultural residues was carried out to determine their use as a substrate for crop cultivation without soil in a protected environment. The selected substrates were Sphagnum peat, coir fiber, and compost, which were managed alone or in mixtures of 50/50, 75/25, or 25/75% v/v ratios. We also included a mixture of virgin mountain soil and earthworm humus (known as INIA mixture) because it is used by local growers. The results showed that the substrates based on coir fiber, peat, and mixtures of both presented suitable characteristics for horticultural crops. On the contrary, compost-based substrates had high pH values and low organic matter contents that could be improved before use. The relationship found between the evaluated parameters of each substrate allowed us to establish that variables, such as the content of organic matter and water at different tensions and particle sizes, can be utilized to make a quick selection of the substrates produced locally, which would lead to the use of waste in a way that is more consistent with sustainable agricultural production and minimal environmental impact, by being used in the production of crops in containers without soil. In addition, these results can be used as an alternative reference in localities where these residues are easily available.