The problem of the use and disposal of horticultural substrates is an important element of the optimization of plastic greenhouse production in terms of economic and environmental efficiency. The production of mineral substrates is associated with a high energy expenditure, which generates costs and greenhouse gas (GHG) emissions. An important factor is also the transport of professional substrates over long distances. The research objective was to evaluate the possibility of using sheep wool to create horticultural substrates in the hydroponic production of cucumber. The modifier of production technology was the use of substrates of various origins. The experiment was based on the use of two substrates: one was a conventional substrate, made of mineral wool, and the other was made of greasy Gissar sheep wool, which is considered waste or a nuisance byproduct of sheep farming today. The adopted functional unit was 1 ton of commercial cucumber yield. The boundaries of the system were soil formation, fertilization, irrigation, and harvesting. The amount of GHG emissions was calculated in accordance with the ISO 14040 and ISO 14044 standards. The results of the experiment show that the use of sheep wool as a substrate in the hydroponic cultivation of cucumbers reduced yield by approximately 8%, but it allowed for a higher efficiency of water and mineral fertilizer use per crop mass unit. Within the adopted system boundary, the value of the carbon footprint in the object with the conventional substrate was 276.9 kg CO2 eq · Mg−1. The value of this parameter for the object with the sheep wool was 193.9 kg CO2 eq · Mg−1. The use of sheep wool did not increase the phytosanitary risk of the cultivated plants. An important goal for achieving sustainability, especially in food production, is to use materials that are easily recyclable and renewable, locally available, and environmentally friendly. The use of sheep wool as a substrate for soilless plastic greenhouse cultivation is a rational solution, as this material consists of 60% animal protein fibers, 10% fat, 15% moisture, 10% sheep sweat, and an average of 5% impurities. This makes it an easily recyclable, easily renewable, and environmentally friendly source of raw material for hydroponic substrates in food production, contrary to rockwool, which produces waste that is difficult to manage and a nuisance to the natural environment. In the countries of Central Asia, the sheep population is over 20 million; therefore, the potential for using sheep wool material for agricultural production is significant.