diff --git a/conan/tools/gnu/autotoolstoolchain.py b/conan/tools/gnu/autotoolstoolchain.py
index df84c6c2d83..58115a6072b 100644
--- a/conan/tools/gnu/autotoolstoolchain.py
+++ b/conan/tools/gnu/autotoolstoolchain.py
@@ -13,9 +13,10 @@
 
 
 class AutotoolsToolchain:
-    def __init__(self, conanfile, namespace=None):
+    def __init__(self, conanfile, namespace=None, prefix="/"):
         self._conanfile = conanfile
         self._namespace = namespace
+        self._prefix = prefix
 
         self.configure_args = self._default_configure_shared_flags() + self._default_configure_install_flags()
         self.autoreconf_args = self._default_autoreconf_flags()
@@ -168,7 +169,7 @@ def _get_argument(argument_name, cppinfo_name):
             return "--{}=${{prefix}}/{}".format(argument_name, elements[0]) if elements else ""
 
         # If someone want arguments but not the defaults can pass them in args manually
-        configure_install_flags.extend(["--prefix=/",
+        configure_install_flags.extend([f"--prefix={self._prefix}",
                                        _get_argument("bindir", "bindirs"),
                                        _get_argument("sbindir", "bindirs"),
                                        _get_argument("libdir", "libdirs"),
diff --git a/conans/test/integration/toolchains/gnu/test_autotoolstoolchain.py b/conans/test/integration/toolchains/gnu/test_autotoolstoolchain.py
index 1b9b3269abe..9c91d3c8ef1 100644
--- a/conans/test/integration/toolchains/gnu/test_autotoolstoolchain.py
+++ b/conans/test/integration/toolchains/gnu/test_autotoolstoolchain.py
@@ -1,3 +1,4 @@
+import os
 import platform
 import textwrap
 
@@ -67,3 +68,28 @@ def generate(self):
     client.save({"conanfile.py": conanfile})
     client.run("install .")
 
+
+def test_set_prefix():
+
+    conanfile = textwrap.dedent("""
+        from conan import ConanFile
+        from conan.tools.gnu import AutotoolsToolchain
+        from conan.tools.layout import basic_layout
+
+
+        class Foo(ConanFile):
+            name = "foo"
+            version = "1.0"
+            def layout(self):
+                basic_layout(self)
+            def generate(self):
+                at_toolchain = AutotoolsToolchain(self, prefix="/somefolder")
+                at_toolchain.generate()
+    """)
+
+    client = TestClient()
+    client.save({"conanfile.py": conanfile})
+    client.run("install .")
+    conanbuild = client.load(os.path.join(client.current_folder, "build", "conan", "conanbuild.conf"))
+    assert "--prefix=/somefolder" in conanbuild
+    assert conanbuild.count("--prefix") == 1