diff --git a/eb_hooks.py b/eb_hooks.py
index d92f457e41..d2aa6e1803 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -14,6 +14,7 @@
 from easybuild.tools.systemtools import AARCH64, POWER, X86_64, get_cpu_architecture, get_cpu_features
 from easybuild.tools.toolchain.compiler import OPTARCH_GENERIC
 from easybuild.tools.version import VERSION as EASYBUILD_VERSION
+from easybuild.tools.modules import get_software_root_env_var_name
 
 # prefer importing LooseVersion from easybuild.tools, but fall back to distuils in case EasyBuild <= 4.7.0 is used
 try:
@@ -519,6 +520,12 @@ def post_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwar
 
 def pre_configure_hook(self, *args, **kwargs):
     """Main pre-configure hook: trigger custom functions based on software name."""
+    eprefix = get_eessi_envvar('EPREFIX')
+
+    for filter_dep_spec in build_option('filter_deps') or []:
+        var_name = get_software_root_env_var_name(filter_dep_spec)
+        env.setvar(var_name, os.path.join(eprefix, 'usr'))
+
     if self.name in PRE_CONFIGURE_HOOKS:
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)