The zinnia (Zinnia elegans Jacq.) is an ornamental plant used in landscape composition and presents great potential for cultivation as a cut flower, potted. Faced with the new trend of integrated flower production, that proposes more environmentally friendly practices aiming at sustainability, there is a need to determine alternative substrates that allow the production of quality seedlings. Therefore, this study aimed to evaluate the vigor and quality of zinnia seedlings produced in alternative substrates in trays with different cell size. Two different types of trays of expanded polystyrene with different cell size were tested as following: 128-cell and 200-cell trays with a volume of 40 cm3 and 16 cm3, respectively. For the growth of the seedlings, three types of substrate were tested: commercial substrate; composting of organic waste; mixture of sand, soil and carbonized rice husk in the proportion of 1:1:1 (v:v:v). The experiment was a completely randomized design, using 24 trays in a factorial arrangement 3x2 (substrate x tray cell size), with four replicate and eight seedling per replicate. The phytotechnical characteristics evaluated were plant height, number of leaves, root length and dry weight of plants, the vigor of seedlings and clod stability was determined by rating scales. The physicochemical and physical proprieties of organic substrate enables produce high quality seedling using 128-cell trays, but the 200-cell trays also produce good quality seedling, having the advantage of using smaller volumes of substrates.