diff --git a/src/cargo/ops/registry/publish.rs b/src/cargo/ops/registry/publish.rs
index 16c0348be65..1abd00a4330 100644
--- a/src/cargo/ops/registry/publish.rs
+++ b/src/cargo/ops/registry/publish.rs
@@ -126,26 +126,7 @@ pub fn publish(ws: &Workspace<'_>, opts: &PublishOpts<'_>) -> CargoResult<()> {
     }
 
     let just_pkgs: Vec<_> = pkgs.iter().map(|p| p.0).collect();
-    let reg_or_index = match opts.reg_or_index.clone() {
-        Some(r) => {
-            validate_registry(&just_pkgs, Some(&r))?;
-            Some(r)
-        }
-        None => {
-            let reg = super::infer_registry(&just_pkgs)?;
-            validate_registry(&just_pkgs, reg.as_ref())?;
-            if let Some(RegistryOrIndex::Registry(registry)) = &reg {
-                if registry != CRATES_IO_REGISTRY {
-                    // Don't warn for crates.io.
-                    opts.gctx.shell().note(&format!(
-                        "found `{}` as only allowed registry. Publishing to it automatically.",
-                        registry
-                    ))?;
-                }
-            }
-            reg
-        }
-    };
+    let reg_or_index = resolve_registry_or_index(opts, &just_pkgs)?;
 
     // This is only used to confirm that we can create a token before we build the package.
     // This causes the credential provider to be called an extra time, but keeps the same order of errors.
@@ -814,6 +795,46 @@ fn package_list(pkgs: impl IntoIterator<Item = PackageId>, final_sep: &str) -> S
     }
 }
 
+fn resolve_registry_or_index(
+    opts: &PublishOpts<'_>,
+    just_pkgs: &[&Package],
+) -> CargoResult<Option<RegistryOrIndex>> {
+    let opt_index_or_registry = opts.reg_or_index.clone();
+
+    let res = match opt_index_or_registry {
+        ref r @ Some(ref registry_or_index) => {
+            validate_registry(just_pkgs, r.as_ref())?;
+
+            let registry_is_specified_by_any_package = just_pkgs
+                .iter()
+                .any(|pkg| pkg.publish().as_ref().map(|v| v.len()).unwrap_or(0) > 0);
+
+            if registry_is_specified_by_any_package && registry_or_index.is_index() {
+                opts.gctx.shell().warn(r#"`--index` will ignore registries set by `package.publish` in Cargo.toml, and may cause unexpected push to prohibited registry
+help: use `--registry` instead or set `publish = true` in Cargo.toml to suppress this warning"#)?;
+            }
+
+            r.clone()
+        }
+        None => {
+            let reg = super::infer_registry(&just_pkgs)?;
+            validate_registry(&just_pkgs, reg.as_ref())?;
+            if let Some(RegistryOrIndex::Registry(registry)) = &reg {
+                if registry != CRATES_IO_REGISTRY {
+                    // Don't warn for crates.io.
+                    opts.gctx.shell().note(&format!(
+                        "found `{}` as only allowed registry. Publishing to it automatically.",
+                        registry
+                    ))?;
+                }
+            }
+            reg
+        }
+    };
+
+    Ok(res)
+}
+
 fn validate_registry(pkgs: &[&Package], reg_or_index: Option<&RegistryOrIndex>) -> CargoResult<()> {
     let reg_name = match reg_or_index {
         Some(RegistryOrIndex::Registry(r)) => Some(r.as_str()),
diff --git a/tests/testsuite/publish.rs b/tests/testsuite/publish.rs
index cbe36d6d83c..aeba4cebf13 100644
--- a/tests/testsuite/publish.rs
+++ b/tests/testsuite/publish.rs
@@ -979,6 +979,60 @@ fn publish_implicitly_to_only_allowed_registry() {
     );
 }
 
+#[cargo_test]
+fn publish_when_both_publish_and_index_specified() {
+    let registry = RegistryBuilder::new()
+        .http_api()
+        .http_index()
+        .alternative()
+        .build();
+
+    let p = project().build();
+
+    let _ = repo(&paths::root().join("foo"))
+        .file(
+            "Cargo.toml",
+            r#"
+                [package]
+                name = "foo"
+                version = "0.0.1"
+                edition = "2015"
+                authors = []
+                license = "MIT"
+                description = "foo"
+                documentation = "foo"
+                homepage = "foo"
+                repository = "foo"
+                publish = ["registry"]
+            "#,
+        )
+        .file("src/main.rs", "fn main() {}")
+        .build();
+
+    p.cargo("publish")
+        .arg("--index")
+        .arg(registry.index_url().as_str())
+        .arg("--token")
+        .arg(registry.token())
+        .with_stderr_data(str![[r#"
+[WARNING] `cargo publish --token` is deprecated in favor of using `cargo login` and environment variables
+[WARNING] `--index` will ignore registries set by `package.publish` in Cargo.toml, and may cause unexpected push to prohibited registry
+[HELP] use `--registry` instead or set `publish = true` in Cargo.toml to suppress this warning
+[UPDATING] [..] index
+[PACKAGING] foo v0.0.1 ([ROOT]/foo)
+[PACKAGED] 5 files, [FILE_SIZE]B ([FILE_SIZE]B compressed)
+[VERIFYING] foo v0.0.1 ([ROOT]/foo)
+[COMPILING] foo v0.0.1 ([ROOT]/foo/target/package/foo-0.0.1)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+[UPLOADING] foo v0.0.1 ([ROOT]/foo)
+[UPLOADED] foo v0.0.1 to registry [..]
+[NOTE] waiting for foo v0.0.1 to be available at registry [..]
+[HELP] you may press ctrl-c to skip waiting; the crate should be available shortly
+[PUBLISHED] foo v0.0.1 at registry [..]
+"#]])
+        .run();
+}
+
 #[cargo_test]
 fn publish_failed_with_index_and_only_allowed_registry() {
     let registry = RegistryBuilder::new()
@@ -1014,6 +1068,7 @@ fn publish_failed_with_index_and_only_allowed_registry() {
         .arg(registry.index_url().as_str())
         .with_status(101)
         .with_stderr_data(str![[r#"
+...
 [ERROR] command-line argument --index requires --token to be specified
 
 "#]])