diff --git a/src/cargo/util/config/mod.rs b/src/cargo/util/config/mod.rs
index 4da14cb1a65..06452f1881a 100644
--- a/src/cargo/util/config/mod.rs
+++ b/src/cargo/util/config/mod.rs
@@ -804,6 +804,15 @@ impl Config {
             self.cli_config = Some(cli_config.iter().map(|s| s.to_string()).collect());
             self.merge_cli_args()?;
         }
+        if self.unstable_flags.config_include {
+            // If the config was already loaded (like when fetching the
+            // `[alias]` table), it was loaded with includes disabled because
+            // the `unstable_flags` hadn't been set up, yet. Any values
+            // fetched before this step will not process includes, but that
+            // should be fine (`[alias]` is one of the only things loaded
+            // before configure). This can be removed when stabilized.
+            self.reload_rooted_at(self.cwd.clone())?;
+        }
         let extra_verbose = verbose >= 2;
         let verbose = verbose != 0;
 
@@ -956,10 +965,10 @@ impl Config {
     /// `seen` is used to check for cyclic includes.
     fn load_includes(&self, mut value: CV, seen: &mut HashSet<PathBuf>) -> CargoResult<CV> {
         // Get the list of files to load.
-        let (includes, def) = match &mut value {
+        let includes = match &mut value {
             CV::Table(table, _def) => match table.remove("include") {
-                Some(CV::String(s, def)) => (vec![(s, def.clone())], def),
-                Some(CV::List(list, def)) => (list, def),
+                Some(CV::String(s, def)) => vec![(s, def.clone())],
+                Some(CV::List(list, _def)) => list,
                 Some(other) => bail!(
                     "`include` expected a string or list, but found {} in `{}`",
                     other.desc(),
@@ -973,8 +982,6 @@ impl Config {
         };
         // Check unstable.
         if !self.cli_unstable().config_include {
-            self.shell().warn(format!("config `include` in `{}` ignored, the -Zconfig-include command-line flag is required",
-                def))?;
             return Ok(value);
         }
         // Accumulate all values here.
diff --git a/tests/testsuite/config_include.rs b/tests/testsuite/config_include.rs
index 933eb1f5ede..aff2a78afd8 100644
--- a/tests/testsuite/config_include.rs
+++ b/tests/testsuite/config_include.rs
@@ -1,22 +1,23 @@
 //! Tests for `include` config field.
 
-use super::config::{
-    assert_error, assert_match, read_output, write_config, write_config_at, ConfigBuilder,
-};
-use cargo_test_support::{no_such_file_err_msg, paths};
+use super::config::{assert_error, write_config, write_config_at, ConfigBuilder};
+use cargo_test_support::{no_such_file_err_msg, paths, project};
 use std::fs;
 
 #[cargo_test]
 fn gated() {
     // Requires -Z flag.
     write_config("include='other'");
+    write_config_at(
+        ".cargo/other",
+        "
+        othervalue = 1
+        ",
+    );
     let config = ConfigBuilder::new().build();
-    let output = read_output(config);
-    let expected = "\
-warning: config `include` in `[..]/.cargo/config` ignored, \
-the -Zconfig-include command-line flag is required
-";
-    assert_match(expected, &output);
+    assert_eq!(config.get::<Option<i32>>("othervalue").unwrap(), None);
+    let config = ConfigBuilder::new().unstable_flag("config-include").build();
+    assert_eq!(config.get::<i32>("othervalue").unwrap(), 1);
 }
 
 #[cargo_test]
@@ -43,6 +44,45 @@ fn simple() {
     assert_eq!(config.get::<i32>("key3").unwrap(), 4);
 }
 
+#[cargo_test]
+fn works_with_cli() {
+    write_config_at(
+        ".cargo/config.toml",
+        "
+        include = 'other.toml'
+        [build]
+        rustflags = ['-W', 'unused']
+        ",
+    );
+    write_config_at(
+        ".cargo/other.toml",
+        "
+        [build]
+        rustflags = ['-W', 'unsafe-code']
+        ",
+    );
+    let p = project().file("src/lib.rs", "").build();
+    p.cargo("build -v")
+        .with_stderr(
+            "\
+[COMPILING] foo v0.0.1 [..]
+[RUNNING] `rustc [..]-W unused`
+[FINISHED] [..]
+",
+        )
+        .run();
+    p.cargo("build -v -Z config-include")
+        .masquerade_as_nightly_cargo()
+        .with_stderr(
+            "\
+[COMPILING] foo v0.0.1 [..]
+[RUNNING] `rustc [..]-W unsafe-code -W unused`
+[FINISHED] [..]
+",
+        )
+        .run();
+}
+
 #[cargo_test]
 fn left_to_right() {
     // How it merges multiple includes.
@@ -77,9 +117,11 @@ fn left_to_right() {
 fn missing_file() {
     // Error when there's a missing file.
     write_config("include='missing'");
-    let config = ConfigBuilder::new().unstable_flag("config-include").build();
+    let config = ConfigBuilder::new()
+        .unstable_flag("config-include")
+        .build_err();
     assert_error(
-        config.get::<i32>("whatever").unwrap_err(),
+        config.unwrap_err(),
         &format!(
             "\
 could not load Cargo configuration
@@ -103,9 +145,11 @@ fn cycle() {
     write_config_at(".cargo/config", "include='one'");
     write_config_at(".cargo/one", "include='two'");
     write_config_at(".cargo/two", "include='config'");
-    let config = ConfigBuilder::new().unstable_flag("config-include").build();
+    let config = ConfigBuilder::new()
+        .unstable_flag("config-include")
+        .build_err();
     assert_error(
-        config.get::<i32>("whatever").unwrap_err(),
+        config.unwrap_err(),
         "\
 could not load Cargo configuration
 
@@ -147,9 +191,11 @@ fn cli_include() {
 fn bad_format() {
     // Not a valid format.
     write_config("include = 1");
-    let config = ConfigBuilder::new().unstable_flag("config-include").build();
+    let config = ConfigBuilder::new()
+        .unstable_flag("config-include")
+        .build_err();
     assert_error(
-        config.get::<i32>("whatever").unwrap_err(),
+        config.unwrap_err(),
         "\
 could not load Cargo configuration