diff --git a/bin/desi_merge_psf b/bin/desi_merge_psf
index 643ca849c..c5f6132f4 100755
--- a/bin/desi_merge_psf
+++ b/bin/desi_merge_psf
@@ -12,6 +12,4 @@ parser.add_argument('-o','--outfile', type = str, default = None, required=True,
 
 args = parser.parse_args()
 
-merge_psf(args.infiles,args.outfile)
-
-
+merge_psf(args.infiles[0],args.infiles[1:],args.outfile)
diff --git a/py/desispec/scripts/proc.py b/py/desispec/scripts/proc.py
index b3b7fad30..795d6ac11 100644
--- a/py/desispec/scripts/proc.py
+++ b/py/desispec/scripts/proc.py
@@ -645,6 +645,9 @@ def main(args=None, comm=None):
                 cmd += ' --input-psf {}'.format(inpsf)
                 cmd += ' --output-psf {}'.format(outpsf)
 
+                if args.dont_merge_with_psf_input :
+                    cmd += ' --dont-merge-with-input'
+
                 # fibers to ignore for the PSF fit
                 # specex uses the fiber index in a camera
                 fibers_to_ignore = badfibers([hdr, camhdr[camera]],["BROKENFIBERS","BADCOLUMNFIBERS"])%500
diff --git a/py/desispec/scripts/specex.py b/py/desispec/scripts/specex.py
index 282cddc73..e8c45ff07 100644
--- a/py/desispec/scripts/specex.py
+++ b/py/desispec/scripts/specex.py
@@ -50,6 +50,9 @@ def parse(options=None):
                         help="comma separated list of broken fibers")
     parser.add_argument("--disable-merge", action = 'store_true',
                         help="disable merging fiber bundles")
+    parser.add_argument("--dont-merge-with-input", action = 'store_true',
+                        help="dont use the input PSF as default when merging bundles")
+
 
     args = parser.parse_args(options)
 
@@ -271,7 +274,11 @@ def main(args=None, comm=None):
             time.sleep(5.)
 
             try:
-                merge_psf(inpsffile, bundlefiles, outfits)
+                if args.dont_merge_with_input :
+                    log.info("Do not include input PSF when merging bundles")
+                    merge_psf(bundlefiles[0], bundlefiles[1:], outfits)
+                else :
+                    merge_psf(inpsffile, bundlefiles, outfits)
             except Exception as e:
                 log.error(e)
                 log.error("merging failed for {}".format(outfits))
diff --git a/py/desispec/workflow/desi_proc_funcs.py b/py/desispec/workflow/desi_proc_funcs.py
index 41989633a..029d45949 100755
--- a/py/desispec/workflow/desi_proc_funcs.py
+++ b/py/desispec/workflow/desi_proc_funcs.py
@@ -89,6 +89,7 @@ def get_shared_desi_proc_parser():
     parser.add_argument("--extract-subcomm-size", type=int, default=None, help="Size to use for GPU extract subcomm")
     parser.add_argument("--no-gpu", action="store_true", help="Do not use GPU for extractions even if available")
     parser.add_argument("--use-specter", action="store_true", help="Use classic specter instead of gpu_specter")
+    parser.add_argument("--dont-merge-with-psf-input", action="store_true", help="Do not merge with PSF input")
     parser.add_argument("--mpistdstars", action="store_true", help="Use MPI parallelism in stdstar fitting instead of multiprocessing")
     parser.add_argument("--no-skygradpca", action="store_true", help="Do not fit sky gradient")
     parser.add_argument("--no-tpcorrparam", action="store_true", help="Do not apply tpcorrparam spatial model or fit tpcorrparam pca terms")