diff --git a/internal/mcp/tools_analyze_hotspots_scope_reads_test.go b/internal/mcp/tools_analyze_hotspots_scope_reads_test.go
new file mode 100644
index 000000000..e5f47f1ae
--- /dev/null
+++ b/internal/mcp/tools_analyze_hotspots_scope_reads_test.go
@@ -0,0 +1,199 @@
+package mcp
+
+import (
+	"context"
+	"fmt"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+
+	"github.com/zzet/gortex/internal/analysis"
+	"github.com/zzet/gortex/internal/graph"
+	"github.com/zzet/gortex/internal/graph/store_sqlite"
+)
+
+type hotspotScopeReader struct {
+	graph.Reader
+	lookedUp []string
+}
+
+func (r *hotspotScopeReader) GetNode(id string) *graph.Node {
+	r.lookedUp = append(r.lookedUp, id)
+	return r.Reader.GetNode(id)
+}
+
+// Real indexing supplies the repo registry and verifies the source-ID invariant
+// for both callable kinds. Extra ranked rows exercise exact totals past the cap.
+func hotspotScopeFixture(t *testing.T, sqlite bool) (*Server, []analysis.HotspotEntry) {
+	t.Helper()
+	body := "package main\ntype T struct{}\nfunc F() {}\nfunc (T) M() {}\n"
+	s, _ := newAnalyzeServer(t, true,
+		analyzeRepoSpec{name: "gortex", workspace: "shared", body: body},
+		analyzeRepoSpec{name: "gortex2", workspace: "shared", body: body},
+		analyzeRepoSpec{name: "gortex@feature", workspace: "feature", body: body},
+	)
+	kinds := map[graph.NodeKind]bool{}
+	for _, n := range s.graph.AllNodes() {
+		if n.Kind == graph.KindFunction || n.Kind == graph.KindMethod {
+			require.Equal(t, n.RepoPrefix, graph.RepoPrefixOfID(n.ID), n.ID)
+			kinds[n.Kind] = true
+		}
+	}
+	require.True(t, kinds[graph.KindFunction])
+	require.True(t, kinds[graph.KindMethod])
+	if sqlite {
+		store, err := store_sqlite.Open(filepath.Join(t.TempDir(), "hotspots.sqlite"))
+		require.NoError(t, err)
+		t.Cleanup(func() { require.NoError(t, store.Close()) })
+		store.AddBatch(s.graph.AllNodes(), s.graph.AllEdges())
+		s.graph = store
+	}
+	var entries []analysis.HotspotEntry
+	for i := range 23 {
+		for _, repo := range []string{"gortex2", "gortex@feature", "gortex"} {
+			ws := "shared"
+			if repo == "gortex@feature" {
+				ws = "feature"
+			}
+			kind := graph.KindFunction
+			if i%2 != 0 {
+				kind = graph.KindMethod
+			}
+			n := &graph.Node{ID: fmt.Sprintf("%s/pkg/hot.go::F%02d", repo, i), Name: fmt.Sprintf("F%02d", i), Kind: kind,
+				FilePath: repo + "/pkg/hot.go", RepoPrefix: repo, WorkspaceID: ws}
+			s.graph.AddNode(n)
+			entries = append(entries, analysis.HotspotEntry{ID: n.ID, Name: n.Name, Kind: string(kind), FilePath: n.FilePath, ComplexityScore: float64(100 - len(entries))})
+		}
+	}
+	// Stub and unknown-prefix rows cannot safely use a slash-derived repo key.
+	for _, n := range []*graph.Node{
+		{ID: "gortex@feature::stdlib::net/http::Get", Kind: graph.KindFunction, RepoPrefix: "gortex@feature", WorkspaceID: "feature", FilePath: "external::net/http"},
+		{ID: "unknown/pkg/legacy.go::F", Kind: graph.KindFunction, RepoPrefix: "gortex", WorkspaceID: "shared", FilePath: "unknown/pkg/legacy.go"},
+	} {
+		s.graph.AddNode(n)
+		entries = append(entries, analysis.HotspotEntry{ID: n.ID, Kind: string(n.Kind), FilePath: n.FilePath})
+	}
+	for repo, callers := range map[string]int{"gortex": 22, "gortex2": 20, "gortex@feature": 18} {
+		for i := 1; i <= callers; i++ {
+			s.graph.AddEdge(&graph.Edge{From: fmt.Sprintf("%s/pkg/hot.go::F%02d", repo, i), To: repo + "/pkg/hot.go::F00", Kind: graph.EdgeCalls})
+		}
+	}
+	installCommunitiesForTest(s, &analysis.CommunityResult{})
+	s.hotspots = entries
+	s.hotspotsReady = true
+	return s, entries
+}
+
+func TestHotspotsScopeSkipsInvisibleRepoReads(t *testing.T) {
+	t.Setenv("GORTEX_DAEMON_MEMRELEASE", "0")
+	for _, backend := range []string{"memory", "sqlite"} {
+		t.Run(backend, func(t *testing.T) {
+			s, cached := hotspotScopeFixture(t, backend == "sqlite")
+			for _, tc := range []struct {
+				name, workspace, repo, mode string
+				bound                       bool
+				threshold                   float64
+				reads, total                int
+			}{
+				{name: "repo", repo: "gortex", reads: 25, total: 24},
+				{name: "workspace", workspace: "shared", bound: true, reads: 48, total: 47},
+				{name: "workspace_repo", workspace: "shared", repo: "gortex2", bound: true, reads: 25, total: 23},
+				{name: "worktree", repo: "gortex@feature", reads: 25, total: 24},
+				{name: "unbound", reads: 0, total: 71},
+				{name: "deny_all", workspace: "missing", bound: true, reads: 2, total: 0},
+				{name: "novelty", repo: "gortex", mode: "novelty", reads: 25, total: 24},
+				{name: "threshold", repo: "gortex", threshold: 50, reads: 1, total: 1},
+			} {
+				t.Run(tc.name, func(t *testing.T) {
+					ctx := WithSessionID(context.Background(), backend+"-"+tc.name)
+					if tc.bound {
+						ss := s.sessionFor(ctx)
+						ss.scopeResolved, ss.scopeBound, ss.scopeWorkspaceID = true, true, tc.workspace
+					}
+					if tc.repo != "" {
+						ctx = withRepoAllow(ctx, map[string]bool{tc.repo: true})
+					}
+					args := map[string]any{"kind": "hotspots", "format": "json", "max_bytes": float64(0), "mode": tc.mode, "threshold": tc.threshold}
+					req := makeReq("analyze", args)
+					entries := cached
+					if tc.threshold != 0 {
+						entries = analysis.FindHotspots(s.graph, s.getCommunities(), tc.threshold)
+						require.NotEmpty(t, entries)
+					}
+					if tc.mode != "" {
+						entries = rerankHotspots(entries, s.graph, tc.mode, "adds", 30)
+					}
+					// The base implementation hydrates every entry before filtering.
+					kept := entries
+					if s.scopeFiltersActive(ctx) {
+						kept = make([]analysis.HotspotEntry, 0, len(entries))
+						for _, e := range entries {
+							if s.analyzeNodeVisible(ctx, s.graph.GetNode(e.ID)) {
+								kept = append(kept, e)
+							}
+						}
+					}
+					total := len(kept)
+					require.Equal(t, tc.total, total)
+					if total > 20 {
+						kept = kept[:20]
+					}
+					want, err := s.respondJSONOrTOON(ctx, req, map[string]any{"hotspots": kept, "total": total, "truncated": total > 20})
+					require.NoError(t, err)
+					reader := &hotspotScopeReader{Reader: s.graph}
+					callCtx := withRequestView(ctx, &requestView{reader: reader})
+					got, err := s.handleFindHotspots(callCtx, req)
+					require.NoError(t, err)
+					require.False(t, got.IsError, toolResultText(got))
+					require.Equal(t, toolResultText(want), toolResultText(got), "complete response must match the base filter")
+					require.Len(t, reader.lookedUp, tc.reads)
+					for _, id := range reader.lookedUp {
+						if id == "gortex@feature::stdlib::net/http::Get" || id == "unknown/pkg/legacy.go::F" {
+							continue
+						}
+						require.True(t, s.analyzeNodeVisible(ctx, s.graph.GetNode(id)), "invisible source entry was hydrated: %s", id)
+					}
+					if tc.threshold == 0 && tc.name != "unbound" {
+						require.Contains(t, reader.lookedUp, "gortex@feature::stdlib::net/http::Get")
+						require.Contains(t, reader.lookedUp, "unknown/pkg/legacy.go::F")
+					}
+				})
+			}
+		})
+	}
+}
+
+func TestHotspotsScopeSingleRepoKeepsUnprefixedReads(t *testing.T) {
+	t.Setenv("GORTEX_DAEMON_MEMRELEASE", "0")
+	for _, backend := range []string{"memory", "sqlite"} {
+		t.Run(backend, func(t *testing.T) {
+			s, _ := newAnalyzeServer(t, true, analyzeRepoSpec{name: "solo", workspace: "solo", body: structuralBody("solo")})
+			require.False(t, s.multiIndexer.IsMultiRepo())
+			if backend == "sqlite" {
+				store, err := store_sqlite.Open(filepath.Join(t.TempDir(), "solo.sqlite"))
+				require.NoError(t, err)
+				t.Cleanup(func() { require.NoError(t, store.Close()) })
+				store.AddBatch(s.graph.AllNodes(), s.graph.AllEdges())
+				s.graph = store
+			}
+			n := &graph.Node{ID: "internal/pkg.go::F", Kind: graph.KindFunction, WorkspaceID: "solo"}
+			s.graph.AddNode(n)
+			require.NotEqual(t, n.RepoPrefix, graph.RepoPrefixOfID(n.ID), "single-repo IDs do not encode repo ownership")
+			installCommunitiesForTest(s, &analysis.CommunityResult{})
+			s.hotspots = []analysis.HotspotEntry{{ID: n.ID}}
+			s.hotspotsReady = true
+			ctx := outlineBoundContext(s, "solo", "solo", nil)
+			req := makeReq("analyze", map[string]any{"format": "json"})
+			want, err := s.respondJSONOrTOON(ctx, req, map[string]any{"hotspots": s.hotspots, "total": 1, "truncated": false})
+			require.NoError(t, err)
+			reader := &hotspotScopeReader{Reader: s.graph}
+			ctx = withRequestView(ctx, &requestView{reader: reader})
+			result, err := s.handleFindHotspots(ctx, req)
+			require.NoError(t, err)
+			require.False(t, result.IsError)
+			require.Equal(t, toolResultText(want), toolResultText(result))
+			require.Equal(t, []string{n.ID}, reader.lookedUp)
+		})
+	}
+}
diff --git a/internal/mcp/tools_enhancements.go b/internal/mcp/tools_enhancements.go
index 65077ef5f..bfaf2486e 100644
--- a/internal/mcp/tools_enhancements.go
+++ b/internal/mcp/tools_enhancements.go
@@ -2734,8 +2734,25 @@ func (s *Server) handleFindHotspots(ctx context.Context, req mcp.CallToolRequest
 	// Strict no-op for an unbound session with no RepoAllow.
 	if s.scopeFiltersActive(ctx) {
 		reader := s.readerFor(ctx)
+		var excludedRepos map[string]bool
+		if s.multiIndexer != nil && s.multiIndexer.IsMultiRepo() {
+			workspaceRepos, bound := s.sessionWorkspaceRepoSet(ctx)
+			allow := repoAllowFromContext(ctx)
+			excludedRepos = make(map[string]bool)
+			for _, prefix := range s.multiIndexer.RepoPrefixes() {
+				if (bound && !workspaceRepos[prefix]) || (len(allow) > 0 && !allow[prefix]) {
+					excludedRepos[prefix] = true
+				}
+			}
+		}
 		kept := make([]analysis.HotspotEntry, 0, len(entries))
 		for _, e := range entries {
+			// Only multi-repo source IDs encode ownership as prefix/path::symbol.
+			// Unprefixed, stub and unknown IDs still need the node visibility check.
+			path, symbol, sourceID := strings.Cut(e.ID, "::")
+			if sourceID && symbol != "" && excludedRepos[graph.RepoPrefixOfID(path)] {
+				continue
+			}
 			if s.analyzeNodeVisible(ctx, reader.GetNode(e.ID)) {
 				kept = append(kept, e)
 			}