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The importance of automatic seedling transplantation in plant-growing companies cannot be overstated. The key step of intelligent transplanting is the effective and precise detection of fresh saplings. To attain good production, dependability, and reproducibility, enterprises use automation extensively. The use of automatic quality control and assurance system results in a procedure that is cost-effective, dependable, and long-lasting. The sapling tray expressing methodology, the unusual disc comparison four-bar duck mouthpiece seeding method, the electric detector for plantlets detection and classification of a seedling plate, the motion detector, stepping motor, and Programmable Logic Controllers (PLC) management system are all used in the creation of an intelligent different planting structure. It could be used to determine if the soil foundation is filled or not using computer logic programming and management, as well as to regulate the automatic seedling plate transportation. The tray is shifted to minimize scooping up vacant soil foundation by skipping the manipulator’s operation path. Jalapeno plants were used to evaluate the system in an indoor environment. The analysis revealed that if the transplantation speed was 90 min per minute, the percentage of successfully seedling harvesting was 88.24% as well as the percentage of leaking was 17.47%, which met the jalapeno transplantation requirements. The annual percentage of leaks was decreased by around 12% relative to the transplantation model without seedlings recognition. The study serves as a valuable resource for the advancement of smart agricultural transplantation techniques and infrastructure.