This paper addresses simultaneous scheduling of jobs, machines and tools considering tool transfer times (TTTs) between machines, to generate best optimal sequences that minimise makespan in a multi-machine flexible manufacturing system (FMS). Performance of FMS is expected to improve by effective utilisation of its resources, by proper integration and synchronisation of their scheduling. Aim of this paper is to address joint scheduling of jobs, machine and tools in an FMS consisting of machines, central tool magazine and tool transporter considering TTTs. Three nature-inspired algorithms namely Symbiotic Organisms Search algorithm, Crow search algorithm and Flower pollination algorithm, are proposed for solving joint jobs, machine and tool scheduling problems considering TTTs between machines with minimum makespan as objective. The proposed algorithms are numerically tested on various problems and results are compared. The results show that FPA algorithm yields better results for simultaneous scheduling of jobs, machines and tools considering TTTs between machines.Keywords: flexible manufacturing systems; simultaneous scheduling of jobs; tools and machines; tool transporter; symbiotic organisms search algorithm; crow search algorithm; flower pollination algorithm.Reference to this paper should be made as follows: Sivarami Reddy, N., Ramamurthy, D.V. and Prahlada Rao, K. (2018) 'Simultaneous scheduling of jobs, machines and tools considering tool transfer times in multi-machine FMS using new nature-inspired algorithms', Int.This paper is a revised and expanded version of a paper entitled 'SOS algorithm for simultaneous scheduling of machines and tools considering tool transfer times in multi machine FMS' presented at ICIS2016,