diff --git a/src/bootstrap/src/core/config/config.rs b/src/bootstrap/src/core/config/config.rs
index 19119a073c5fa..d13dc9d1d177a 100644
--- a/src/bootstrap/src/core/config/config.rs
+++ b/src/bootstrap/src/core/config/config.rs
@@ -360,7 +360,7 @@ pub enum RustfmtState {
     LazyEvaluated,
 }
 
-#[derive(Debug, Default, Clone, Copy, PartialEq)]
+#[derive(Debug, Default, Clone, Copy, PartialEq, Eq)]
 pub enum LlvmLibunwind {
     #[default]
     No,
@@ -381,7 +381,7 @@ impl FromStr for LlvmLibunwind {
     }
 }
 
-#[derive(Default, Copy, Clone, PartialEq, Eq, PartialOrd, Ord, Hash)]
+#[derive(Debug, Default, Copy, Clone, PartialEq, Eq, PartialOrd, Ord, Hash)]
 pub enum SplitDebuginfo {
     Packed,
     Unpacked,
@@ -542,7 +542,7 @@ impl PartialEq<&str> for TargetSelection {
 }
 
 /// Per-target configuration stored in the global configuration structure.
-#[derive(Default, Clone)]
+#[derive(Debug, Default, Clone, PartialEq, Eq)]
 pub struct Target {
     /// Some(path to llvm-config) if using an external LLVM.
     pub llvm_config: Option<PathBuf>,
@@ -644,7 +644,20 @@ impl Merge for TomlConfig {
         do_merge(&mut self.llvm, llvm, replace);
         do_merge(&mut self.rust, rust, replace);
         do_merge(&mut self.dist, dist, replace);
-        assert!(target.is_none(), "merging target-specific config is not currently supported");
+
+        match (self.target.as_mut(), target) {
+            (_, None) => {}
+            (None, Some(target)) => self.target = Some(target),
+            (Some(original_target), Some(new_target)) => {
+                for (triple, new) in new_target {
+                    if let Some(original) = original_target.get_mut(&triple) {
+                        original.merge(new, replace);
+                    } else {
+                        original_target.insert(triple, new);
+                    }
+                }
+            }
+        }
     }
 }
 
@@ -899,7 +912,7 @@ define_config! {
     }
 }
 
-#[derive(Clone, Debug, Deserialize)]
+#[derive(Clone, Debug, Deserialize, PartialEq, Eq)]
 #[serde(untagged)]
 pub enum StringOrBool {
     String(String),
diff --git a/src/bootstrap/src/core/config/tests.rs b/src/bootstrap/src/core/config/tests.rs
index 59e16b6542728..c4073910623a4 100644
--- a/src/bootstrap/src/core/config/tests.rs
+++ b/src/bootstrap/src/core/config/tests.rs
@@ -1,5 +1,7 @@
 use super::{flags::Flags, ChangeIdWrapper, Config};
 use crate::core::build_steps::clippy::get_clippy_rules_in_order;
+use crate::core::config::Target;
+use crate::core::config::TargetSelection;
 use crate::core::config::{LldMode, TomlConfig};
 
 use clap::CommandFactory;
@@ -124,6 +126,10 @@ fn override_toml() {
             "--set=build.gdb=\"bar\"".to_owned(),
             "--set=build.tools=[\"cargo\"]".to_owned(),
             "--set=llvm.build-config={\"foo\" = \"bar\"}".to_owned(),
+            "--set=target.x86_64-unknown-linux-gnu.runner=bar".to_owned(),
+            "--set=target.x86_64-unknown-linux-gnu.rpath=false".to_owned(),
+            "--set=target.aarch64-unknown-linux-gnu.sanitizers=false".to_owned(),
+            "--set=target.aarch64-apple-darwin.runner=apple".to_owned(),
         ],
         |&_| {
             toml::from_str(
@@ -140,6 +146,17 @@ tools = []
 [llvm]
 download-ci-llvm = false
 build-config = {}
+
+[target.aarch64-unknown-linux-gnu]
+sanitizers = true
+rpath = true
+runner = "aarch64-runner"
+
+[target.x86_64-unknown-linux-gnu]
+sanitizers = true
+rpath = true
+runner = "x86_64-runner"
+
                 "#,
             )
             .unwrap()
@@ -163,6 +180,30 @@ build-config = {}
         [("foo".to_string(), "bar".to_string())].into_iter().collect(),
         "setting dictionary value"
     );
+
+    let x86_64 = TargetSelection::from_user("x86_64-unknown-linux-gnu");
+    let x86_64_values = Target {
+        sanitizers: Some(true),
+        rpath: Some(false),
+        runner: Some("bar".into()),
+        ..Default::default()
+    };
+    let aarch64 = TargetSelection::from_user("aarch64-unknown-linux-gnu");
+    let aarch64_values = Target {
+        sanitizers: Some(false),
+        rpath: Some(true),
+        runner: Some("aarch64-runner".into()),
+        ..Default::default()
+    };
+    let darwin = TargetSelection::from_user("aarch64-apple-darwin");
+    let darwin_values = Target { runner: Some("apple".into()), ..Default::default() };
+    assert_eq!(
+        config.target_config,
+        [(x86_64, x86_64_values), (aarch64, aarch64_values), (darwin, darwin_values)]
+            .into_iter()
+            .collect(),
+        "setting dictionary value"
+    );
 }
 
 #[test]