diff --git i/mesonbuild/backend/backends.py w/mesonbuild/backend/backends.py
index ee5f4463a..4100c54c9 100644
--- i/mesonbuild/backend/backends.py
+++ w/mesonbuild/backend/backends.py
@@ -23,6 +23,7 @@ import pickle
 import re
 import typing as T
 import hashlib
+import copy
 
 from .. import build
 from .. import dependencies
@@ -1429,7 +1430,19 @@ class Backend:
                         d.targets.append(i)
 
     def generate_custom_install_script(self, d: InstallData) -> None:
-        d.install_scripts = self.build.install_scripts
+        result: T.List[ExecutableSerialisation] = []
+        srcdir = self.environment.get_source_dir()
+        builddir = self.environment.get_build_dir()
+        for i in self.build.install_scripts:
+            fixed_args = []
+            for a in i.cmd_args:
+                a = a.replace('@SOURCE_ROOT@', srcdir)
+                a = a.replace('@BUILD_ROOT@', builddir)
+                fixed_args.append(a)
+            es = copy.copy(i)
+            es.cmd_args = fixed_args
+            result.append(es)
+        d.install_scripts = result
 
     def generate_header_install(self, d: InstallData) -> None:
         incroot = self.environment.get_includedir()