diff --git a/create_lmodrc.py b/create_lmodrc.py
index 28ad2a1915..1720b762f0 100755
--- a/create_lmodrc.py
+++ b/create_lmodrc.py
@@ -33,6 +33,12 @@ def error(msg):
     error("Prefix directory %s does not exist!" % prefix)
 
 lmodrc_path = os.path.join(prefix, DOT_LMOD, 'lmodrc.lua')
+# Lmod itself doesn't care about the accelerator subdir so remove this duplication from
+# the target path (if it exists)
+accel_subdir = os.getenv("EESSI_ACCELERATOR_TARGET")
+if accel_subdir:
+    lmodrc_path = lmodrc_path.replace("/accel/%s" % accel_subdir, '')
+
 lmodrc_txt = TEMPLATE_LMOD_RC % {
     'dot_lmod': DOT_LMOD,
     'prefix': prefix,
diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 62f073c9a6..11ca614be5 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -8,7 +8,7 @@
 
 DOT_LMOD = '.lmod'
 
-hook_txt ="""require("strict")
+hook_txt = """require("strict")
 local hook = require("Hook")
 local open = io.open
 
@@ -36,7 +36,7 @@
         -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
         -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
         local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
-        
+
        -- Check if the full modulepath starts with the eessi_prefix_*
         return string.find(t.fn, "^" .. eessi_prefix) ~= nil or string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil
     end
@@ -103,7 +103,7 @@
     if isFile(archSitePackage) then
         dofile(archSitePackage)
     end
-    
+
 end
 
 
@@ -111,7 +111,7 @@
     local frameStk  = require("FrameStk"):singleton()
     local mt        = frameStk:mt()
     local simpleName = string.match(t.modFullName, "(.-)/")
-    -- If we try to load CUDA itself, check if the full CUDA SDK was installed on the host in host_injections. 
+    -- If we try to load CUDA itself, check if the full CUDA SDK was installed on the host in host_injections.
     -- This is required for end users to build additional CUDA software. If the full SDK isn't present, refuse
     -- to load the CUDA module and print an informative message on how to set up GPU support for EESSI
     local refer_to_docs = "For more information on how to do this, see https://www.eessi.io/docs/gpu/.\\n"
@@ -207,6 +207,7 @@
 load_site_specific_hooks()
 """
 
+
 def error(msg):
     sys.stderr.write("ERROR: %s\n" % msg)
     sys.exit(1)
@@ -221,12 +222,18 @@ def error(msg):
     error("Prefix directory %s does not exist!" % prefix)
 
 sitepackage_path = os.path.join(prefix, DOT_LMOD, 'SitePackage.lua')
+
+# Lmod itself doesn't care about compute capability so remove this duplication from
+# the install path (if it exists)
+accel_subdir = os.getenv("EESSI_ACCELERATOR_TARGET")
+if accel_subdir:
+    sitepackage_path = sitepackage_path.replace("/accel/%s" % accel_subdir, '')
 try:
     os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True)
     with open(sitepackage_path, 'w') as fp:
         fp.write(hook_txt)
     # Make sure that the created Lmod file has "read/write" for the user/group and "read" permissions for others
-    os.chmod(sitepackage_path, S_IREAD|S_IWRITE|S_IRGRP|S_IWGRP|S_IROTH)
+    os.chmod(sitepackage_path, S_IREAD | S_IWRITE | S_IRGRP | S_IWGRP | S_IROTH)
 
 except (IOError, OSError) as err:
     error("Failed to create %s: %s" % (sitepackage_path, err))