In this paper, the fractional closed-loop system identification using the indirect approach is presented. A bias correction method is developed to deal with the bias problem in the continuous-time fractional closed-loop system identification. This method is based on the least squares estimator combined with the state variable filter approach. The basic idea is to eliminate the estimation bias by adding a correction term in the least squares estimates. The proposed algorithm is extended, using a nonlinear optimization algorithm, to estimate both coefficients and commensurate-order of the process. Numerical example shows the performances of the fractional order bias eliminated least squares method via Monte Carlo simulations. (C) 2015 Elsevier Ltd. All rights reserved.