diff --git a/src/index/mod.rs b/src/index/mod.rs
index 8b08428..f6259b6 100644
--- a/src/index/mod.rs
+++ b/src/index/mod.rs
@@ -56,8 +56,15 @@ pub fn ensure_project(conn: &Connection, root: &Path) -> anyhow::Result<i64> {
 
 /// Detect the project root by walking up from `start` looking for marker files.
 ///
-/// Search order: `.cora.yaml` → `Cargo.toml` → `package.json` → `.git` (dir or file).
-/// Returns the directory containing the first marker found, or `None` if none is found.
+/// Resolution order:
+/// 1. `.cora.yaml` — explicit user override, always wins immediately.
+/// 2. A `Cargo.toml` declaring a `[workspace]` section — a Rust workspace root
+///    beats a nested member crate's plain `Cargo.toml`, so indexing from inside
+///    `crates/*` and resolving from the repo root land on the same project (#522).
+/// 3. The first plain marker (`Cargo.toml`, `package.json`, `.git`) as fallback.
+///
+/// The walk never climbs past a git repository boundary, so an unrelated
+/// `[workspace]` outside the repo cannot hijack resolution.
 pub fn resolve_project_root(start: &Path) -> Option<std::path::PathBuf> {
     let dir = if start.is_file() {
         start.parent()?
@@ -65,22 +72,52 @@ pub fn resolve_project_root(start: &Path) -> Option<std::path::PathBuf> {
         start
     };
 
-    const MARKERS: &[&str] = &[".cora.yaml", "Cargo.toml", "package.json", ".git"];
-
     let mut current = dir.to_path_buf();
+    let mut fallback: Option<std::path::PathBuf> = None;
     loop {
-        for marker in MARKERS {
-            let candidate = current.join(marker);
-            if candidate.exists() {
-                debug!(root = %current.display(), marker, "detected project root");
-                return Some(current);
+        // 1. Explicit cora config wins immediately.
+        if current.join(".cora.yaml").is_file() {
+            debug!(root = %current.display(), marker = ".cora.yaml", "detected project root");
+            return Some(current);
+        }
+
+        // 2. Cargo workspace root beats a nested member crate manifest.
+        let cargo_toml = current.join("Cargo.toml");
+        if cargo_toml.is_file()
+            && std::fs::read_to_string(&cargo_toml)
+                .map(|s| s.contains("[workspace"))
+                .unwrap_or(false)
+        {
+            debug!(root = %current.display(), marker = "[workspace] Cargo.toml", "detected project root");
+            return Some(current);
+        }
+
+        // 3. First plain marker is the fallback (original behavior).
+        if fallback.is_none() {
+            const MARKERS: &[&str] = &["Cargo.toml", "package.json", ".git"];
+            for marker in MARKERS {
+                if current.join(marker).exists() {
+                    fallback = Some(current.clone());
+                    break;
+                }
             }
         }
+
+        // Repo boundary: stop AFTER giving this directory its own chance to
+        // match above (a repo root can legitimately be the workspace root).
+        if current.join(".git").exists() {
+            break;
+        }
         match current.parent() {
             Some(parent) if parent != current => current = parent.to_path_buf(),
-            _ => return None,
+            _ => break,
         }
     }
+
+    if let Some(root) = &fallback {
+        debug!(root = %root.display(), "detected project root");
+    }
+    fallback
 }
 
 /// Resolve `project_id` from the current directory, using project root detection.
@@ -806,4 +843,107 @@ pub struct AuthService {
             "resolved root should contain Cargo.toml"
         );
     }
+
+    /// Regression (#522): running `cora index` from inside a workspace member
+    /// crate must resolve to the WORKSPACE root (the member's plain
+    /// `Cargo.toml` is not the project root), so CLI and MCP agree on one
+    /// project_id instead of silently creating two.
+    #[test]
+    fn test_resolve_project_root_prefers_workspace_root() {
+        let tmp = tempfile::TempDir::new().unwrap();
+        let ws = tmp.path().join("ws");
+        let member = ws.join("crates").join("app");
+        std::fs::create_dir_all(&member).unwrap();
+
+        std::fs::write(
+            ws.join("Cargo.toml"),
+            "[workspace]\nmembers = [\"crates/*\"]\n",
+        )
+        .unwrap();
+        std::fs::write(member.join("Cargo.toml"), "[package]\nname = \"app\"\n").unwrap();
+        std::fs::write(member.join("src.rs"), "fn main() {}\n").unwrap();
+
+        let resolved = resolve_project_root(&member);
+        assert_eq!(
+            resolved.as_deref(),
+            Some(ws.as_path()),
+            "workspace root should win over a member crate's plain Cargo.toml"
+        );
+    }
+
+    /// An explicit `.cora.yaml` anywhere along the walk always wins — it is a
+    /// deliberate user override of project-root detection.
+    #[test]
+    fn test_resolve_project_root_cora_yaml_wins_over_workspace() {
+        let tmp = tempfile::TempDir::new().unwrap();
+        let ws = tmp.path().join("ws");
+        let member = ws.join("crates").join("app");
+        std::fs::create_dir_all(&member).unwrap();
+
+        std::fs::write(
+            ws.join("Cargo.toml"),
+            "[workspace]\nmembers = [\"crates/*\"]\n",
+        )
+        .unwrap();
+        std::fs::write(ws.join(".cora.yaml"), "version: 1\n").unwrap();
+        std::fs::write(member.join("Cargo.toml"), "[package]\nname = \"app\"\n").unwrap();
+        std::fs::write(member.join(".cora.yaml"), "version: 1\n").unwrap();
+
+        let resolved = resolve_project_root(&member);
+        assert_eq!(resolved.as_deref(), Some(member.as_path()));
+    }
+
+    /// Root detection must not climb above a git repository boundary: an
+    /// unrelated `[workspace]` Cargo.toml outside the repo must never hijack
+    /// resolution.
+    #[test]
+    fn test_resolve_project_root_stops_at_git_boundary() {
+        let tmp = tempfile::TempDir::new().unwrap();
+        let outer_ws = tmp.path().join("outer");
+        let repo = outer_ws.join("myrepo");
+        std::fs::create_dir_all(repo.join(".git")).unwrap();
+
+        std::fs::write(
+            outer_ws.join("Cargo.toml"),
+            "[workspace]\nmembers = [\"*\"]\n",
+        )
+        .unwrap();
+        // Repo itself has no markers other than .git and one plain file dir.
+        let deep = repo.join("src");
+        std::fs::create_dir_all(&deep).unwrap();
+
+        let resolved = resolve_project_root(&deep);
+        assert_eq!(
+            resolved.as_deref(),
+            Some(repo.as_path()),
+            ".git must stop the upward walk"
+        );
+    }
+
+    /// Regression (#522): an incremental no-op re-index (all fingerprints
+    /// match) must keep reporting the STORED symbol count — DB state must
+    /// survive untouched re-runs.
+    #[test]
+    fn test_incremental_index_preserves_counts() {
+        let conn = mem_conn();
+        let tmp = tempfile::tempdir().unwrap();
+        let root = tmp.path().to_path_buf();
+        std::fs::write(root.join("lib.rs"), "pub fn alpha() {} pub fn beta() {}\n").unwrap();
+
+        let first = index_project(&conn, &root, false).unwrap();
+        assert_eq!(first.files_indexed, 1);
+        assert!(first.symbols_indexed > 0);
+
+        // Second run: everything unchanged → skipped, nothing wiped.
+        let second = index_project(&conn, &root, false).unwrap();
+        assert_eq!(second.files_skipped, 1);
+        assert_eq!(second.files_indexed, 0);
+
+        let summary = index_stats(&conn, ensure_project(&conn, &root).unwrap()).unwrap();
+        assert_eq!(
+            summary.total_symbols as usize, first.symbols_indexed,
+            "stored symbols must survive an incremental no-op re-run"
+        );
+        assert_eq!(summary.total_files, 1);
+    }
 }
diff --git a/src/main.rs b/src/main.rs
index 507da76..83ab980 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -787,17 +787,40 @@ async fn main() -> Result<()> {
                     verbose || cli.global.verbose,
                     skip_patterns.as_deref(),
                 )?;
-                eprintln!(
-                    "{}",
-                    format!(
-                        "✅ Indexed {} symbols from {} files ({} skipped, {} errors)",
-                        stats.symbols_indexed,
-                        stats.files_indexed,
-                        stats.files_skipped,
-                        stats.errors
-                    )
-                    .green()
-                );
+                if stats.files_indexed == 0 && stats.errors == 0 {
+                    // Incremental no-op: fingerprints all matched. Report the
+                    // STORED totals instead of a confusing zeros line (#522).
+                    eprintln!(
+                        "{}",
+                        format!(
+                            "✓ Index up to date ({} files unchanged)",
+                            stats.files_skipped
+                        )
+                        .green()
+                    );
+                    if let Ok(summary) = index::index_stats(&conn, project_id) {
+                        eprintln!(
+                            "{}",
+                            format!(
+                                "   {} symbols across {} files",
+                                summary.total_symbols, summary.total_files
+                            )
+                            .dimmed()
+                        );
+                    }
+                } else {
+                    eprintln!(
+                        "{}",
+                        format!(
+                            "✅ Indexed {} symbols from {} files ({} skipped, {} errors)",
+                            stats.symbols_indexed,
+                            stats.files_indexed,
+                            stats.files_skipped,
+                            stats.errors
+                        )
+                        .green()
+                    );
+                }
                 eprintln!(
                     "{}",
                     format!(
diff --git a/src/mcp/tools.rs b/src/mcp/tools.rs
index c93d780..8d5fddb 100644
--- a/src/mcp/tools.rs
+++ b/src/mcp/tools.rs
@@ -707,7 +707,7 @@ fn handle_index_status() -> ToolResult {
 
     match crate::index::index_stats(&conn, project_id) {
         Ok(stats) => {
-            let json = serde_json::json!({
+            let mut json = serde_json::json!({
                 "exists": true,
                 "total_symbols": stats.total_symbols,
                 "total_files": stats.total_files,
@@ -715,12 +715,62 @@ fn handle_index_status() -> ToolResult {
                 "symbols_by_kind": stats.symbols_by_kind,
                 "symbols_by_language": stats.symbols_by_language,
             });
+            if let Some(hint) = project_root_mismatch_hint(&conn, project_id, stats.total_symbols) {
+                json["hint"] = serde_json::json!(hint);
+            }
             ToolResult::text(serde_json::to_string_pretty(&json).unwrap_or_default())
         }
         Err(e) => ToolResult::error(format!("Failed to get stats: {e}")),
     }
 }
 
+/// Surface a silent project-root mismatch (#522): the resolved project has no
+/// indexed symbols while other indexed projects in the same global DB do —
+/// usually because CLI and MCP resolved different project roots.
+fn project_root_mismatch_hint(
+    conn: &rusqlite::Connection,
+    project_id: i64,
+    total_symbols: usize,
+) -> Option<String> {
+    if total_symbols > 0 {
+        return None;
+    }
+
+    let mut stmt = conn
+        .prepare(
+            "SELECT p.root_path, COUNT(s.id)
+             FROM projects p
+             JOIN symbols s ON s.project_id = p.id
+             WHERE p.id != ?1
+             GROUP BY p.id
+             ORDER BY COUNT(s.id) DESC
+             LIMIT 3",
+        )
+        .ok()?;
+    let rows: Vec<(String, i64)> = stmt
+        .query_map([project_id], |row| {
+            Ok((row.get::<_, String>(0)?, row.get::<_, i64>(1)?))
+        })
+        .ok()?
+        .filter_map(|r| r.ok())
+        .collect();
+
+    if rows.is_empty() {
+        return None;
+    }
+
+    let list: Vec<String> = rows
+        .iter()
+        .map(|(root, n)| format!("{root} ({n} symbols)"))
+        .collect();
+    Some(format!(
+        "This project root has 0 indexed symbols, but the global index holds data for \
+         other roots: {}. Likely a project-root mismatch between where 'cora index' ran \
+         and where this session resolved the root. Run 'cora index' at your project root.",
+        list.join(", ")
+    ))
+}
+
 // ─── Review Pipeline Handlers (Phase 2) ───
 
 fn handle_review_diff(params: &serde_json::Value) -> ToolResult {
@@ -1160,6 +1210,46 @@ mod tests {
         assert!(result.is_error || result.content[0].text.contains("total_symbols"));
     }
 
+    /// Regression (#522): when the resolved project has zero symbols but the
+    /// global DB holds data for other roots, index_status must carry a hint
+    /// naming those roots instead of silently reporting zeros.
+    #[test]
+    fn project_root_mismatch_hint_on_zero_symbol_project() {
+        let conn = rusqlite::Connection::open_in_memory().unwrap();
+        crate::index::schema::run_migrations(&conn).unwrap();
+
+        let indexed_pid =
+            crate::index::schema::get_or_create_project(&conn, "/workspace/uteke").unwrap();
+        conn.execute(
+            "INSERT INTO symbols (name, kind, file, line, signature, language, project_id)
+             VALUES ('alpha', 'function', 'lib.rs', 1, '', 'rust', ?1)",
+            [indexed_pid],
+        )
+        .unwrap();
+        let empty_pid =
+            crate::index::schema::get_or_create_project(&conn, "/workspace/uteke/crates/app")
+                .unwrap();
+
+        let hint = project_root_mismatch_hint(&conn, empty_pid, 0);
+        assert!(
+            hint.is_some(),
+            "zero-symbol project beside an indexed one must hint"
+        );
+        let hint = hint.unwrap();
+        assert!(
+            hint.contains("/workspace/uteke"),
+            "hint should name the root that actually holds data: {hint}"
+        );
+        assert!(
+            hint.contains("(1 symbols)"),
+            "hint should include counts: {hint}"
+        );
+
+        // Happy paths produce no hint.
+        assert!(project_root_mismatch_hint(&conn, empty_pid, 5).is_none());
+        assert!(project_root_mismatch_hint(&conn, indexed_pid, 1).is_none());
+    }
+
     #[test]
     fn handle_search_symbols_missing_query() {
         let result = handle_tool_call("cora.search_symbols", &serde_json::json!({}));