This paper deals with machines, automated guided vehicles and tools simultaneous scheduling in multi-machine flexible manufacturing system considering jobs' transport times among machines to minimize makespan. Only one copy of every tool type is made available due to economic restrictions. The tools are stored in central tool magazine that shares with and serves for several machines. This simultaneous scheduling problem is highly complex in nature as it involves the allocation of automated guided vehicles and tools to job-operations, job-operations sequencing on machines, and associated trip operations including the dead heading trip and loaded trip times of automated guided vehicles. This paper proposes symbiotic organisms search algorithm for solving this problem. An industrial problem in a manufacturing company is used for verification. The results show that SOSA is providing better solutions than Jaya algorithm, and the obtained schedule can be implemented practically with reduction in cost.