Abstract This paper focuses on the inner iteration that arises in inexact inverse subspace iteration for computing a small deflating subspace of a large matrix pencil. First, it is shown that the method achieves linear rate of convergence if the inner iteration is performed with increasing accuracy. Then, as inner iteration, block-GMRES is used with preconditioners generalizing the one by Robbé, Sadkane and Spence [Inexact inverse subspace iteration with preconditioning applied to non-Hermitian eigenvalue problems, SIAM J. Matrix Anal. Appl. 31 2009, 1, 92–113]. It is shown that the preconditioners help to maintain the number of iterations needed by block-GMRES to approximately a small constant. The efficiency of the preconditioners is illustrated by numerical examples.