As high-input systems, plant production facilities for liner and container plants use large quantities of water, fertilizers, chemical pesticides, plastics, and labor. The use of renewable and biodegradable inputs for growing aesthetically pleasing and healthy plants could potentially improve the economic, environmental, and social sustainability of current production systems. However, costs for production components to integrate sustainable practices into established systems have not been fully explored to date. Our objectives were to determine the economic costs of commercial production systems using alternative containers in aboveground nursery systems. We determined the cost of production (COP) budgets for two woody plant species grown in several locations across the United States. Plants were grown in plastic pots and various alternative pots made from wood pulp (WP), fabric (FB), keratin (KT), and coconut fiber (coir). Cost of production inputs for aboveground nursery systems included the plant itself (liner), liner shipping costs, pot, pot shipping costs, substrate, substrate shipping costs, municipal water, and labor. Our results show that the main difference in the COP is the price of the pot. Although alternative containers could potentially increase water demands, water is currently an insignificant cost in relation to the entire production process. Use of alternative containers could reduce the carbon, water, and chemical footprints of nurseries and greenhouses; however, the cost of alternative containers must become more competitive with plastic to make them an acceptable routine choice for commercial growers.