diff --git a/src/path/mod.rs b/src/path/mod.rs
index 333a4d57..2fa5af2b 100644
--- a/src/path/mod.rs
+++ b/src/path/mod.rs
@@ -150,12 +150,16 @@ impl Expression {
         let parent = self.get_mut_forcibly(root);
         match value.kind {
             ValueKind::Table(ref incoming_map) => {
+                // If the parent is nil, treat it as an empty table
+                if matches!(parent.kind, ValueKind::Nil) {
+                    *parent = Map::<String, Value>::new().into();
+                }
+
                 // Continue the deep merge
                 for (key, val) in incoming_map {
                     Self::root(key.clone()).set(parent, val.clone());
                 }
             }
-
             _ => {
                 *parent = value;
             }
diff --git a/tests/testsuite/file_toml.rs b/tests/testsuite/file_toml.rs
index 6c3980c5..9e89fb0c 100644
--- a/tests/testsuite/file_toml.rs
+++ b/tests/testsuite/file_toml.rs
@@ -1,5 +1,7 @@
 #![cfg(feature = "toml")]
 
+use std::collections::BTreeMap;
+
 use chrono::{DateTime, TimeZone, Utc};
 use float_cmp::ApproxEqUlps;
 use serde_derive::Deserialize;
@@ -422,6 +424,60 @@ bar = "bar is a lowercase param"
     );
 }
 
+#[test]
+fn test_override_empty_tables() {
+    #[derive(Debug, Deserialize)]
+    struct Settings {
+        profile: BTreeMap<String, Profile>,
+    }
+
+    #[derive(Debug, Default, Deserialize)]
+    struct Profile {
+        name: Option<String>,
+    }
+
+    // Test a few scenarios with empty tables:
+    // * foo: empty table -> table with k/v
+    // * bar: table with k/v -> empty table
+    // * baz: empty table relying on Default impl
+    let cfg = Config::builder()
+        .add_source(File::from_str(
+            r#"
+            [profile.foo]
+"#,
+            FileFormat::Toml,
+        ))
+        .add_source(File::from_str(
+            r#"
+            [profile.foo]
+            name = "foo"
+"#,
+            FileFormat::Toml,
+        ))
+        .add_source(File::from_str(
+            r#"
+            [profile.bar]
+            name = "bar"
+"#,
+            FileFormat::Toml,
+        ))
+        .add_source(File::from_str(
+            r#"
+            [profile.bar]
+            [profile.baz]
+"#,
+            FileFormat::Toml,
+        ))
+        .build()
+        .unwrap();
+
+    let settings: Settings = cfg.try_deserialize().unwrap();
+    assert_eq!(settings.profile.len(), 3);
+    assert_eq!(settings.profile["foo"].name.as_deref(), Some("foo"));
+    assert_eq!(settings.profile["bar"].name.as_deref(), Some("bar"));
+    assert_eq!(settings.profile["baz"].name.as_deref(), None);
+}
+
 #[test]
 fn toml() {
     let s = Config::builder()