Deconvolution microscopy is a very useful technique allowing to deblur microscopy images and increase both lateral and axial resolution. It is a software-based technique, and it can be used with most of fluorescence microscopy imaging techniques. By increasing axial resolution, it also enables 3D imaging using a regular wide-field fluorescence microscope. Unfortunately, commercially available deconvolution software are expensive, while freely available ones have limited capabilities of batch file processing. In this work we present BatchDeconvolution, a Fiji plugin that bridges two programs used subsequently in image deconvolution: PSF Generator and DeconvolutionLab2 from Biomedical Imaging Group, EPFL, and provides a simple way to perform batch processing of multiple microscopy files.