diff --git a/SConstruct b/SConstruct
index 9c48ee822..7cd0a051f 100644
--- a/SConstruct
+++ b/SConstruct
@@ -1355,8 +1355,8 @@ if env['layout'] == 'debian':
                                    env['libdirname'], 'cantera', 'matlab', 'toolbox')
 
     env['inst_python_bindir'] = pjoin(base, 'cantera-python', 'usr', 'bin')
-    env['python_prefix'] = pjoin(base, 'cantera-python', 'usr')
-    env['python3_prefix'] = pjoin(base, 'cantera-python3', 'usr')
+    env['python_prefix'] = pjoin(base, 'cantera-python')
+    env['python3_prefix'] = pjoin(base, 'cantera-python3')
 else:
     env['inst_libdir'] = pjoin(instRoot, env['libdirname'])
     env['inst_bindir'] = pjoin(instRoot, 'bin')
diff --git a/interfaces/cython/SConscript b/interfaces/cython/SConscript
index 5fec21aa7..7068f88a3 100644
--- a/interfaces/cython/SConscript
+++ b/interfaces/cython/SConscript
@@ -118,6 +118,7 @@ def install_module(prefix, python_version):
           env['install_python2_action'] = mod_inst
 
     elif localenv['PYTHON_INSTALLER'] == 'debian':
+        extra = localenv.subst(' --root=${python%s_prefix}' % ver)
         install(localenv.Command, dummy, mod,
                 build_cmd + ' install --install-layout=deb --no-compile %s' % extra)
         env['python%s_module_loc' % ver] = '<unspecified>'