In order to minimize makespan (Cmax) without causing tool delay with the fewest copies of each tool type, this study investigates the concurrent scheduling of automated guided vehicles (AGVs), machines (MCs), tool transporter (TT), and tools in a multi-machine flexible manufacturing system (FMS). The tools are housed in a central tool magazine (CTM), accessible to and utilized by several machines. AGVs and the tool transporter (TT) move jobs and tools between machines. Since it involves allocating tool copies and AGVs to job operations, sequencing job operations on machines, and related trip operations, such as AGVs’ and TT’s empty trip and loaded trip times, this simultaneous scheduling problem is highly complicated. This issue is resolved using the symbiotic organisms search algorithm (SOSA), based on the symbiotic interaction strategies that organisms adapt to survive in the ecosystem. This study proposes a mixed nonlinear integer programming formulation to address this problem. Verification is performed using an industrial problem from a manufacturing organization. The results show that employing two copies for two tool types out of 22 tool kinds and one copy for the remaining tool types results in no tool delay, which causes a reduction in the Cmax as well as cost. The industries that can benefit directly from this study are consumer electronics manufacturers, original equipment manufacturers, automobile manufacturers, and textile machine producers. The results demonstrate that the SOSA provides promising results compared to the flower pollination algorithm (FPA).