diff --git a/internal/tools/exec_memory_hints.go b/internal/tools/exec_memory_hints.go
new file mode 100644
index 00000000..f4710e7c
--- /dev/null
+++ b/internal/tools/exec_memory_hints.go
@@ -0,0 +1,47 @@
+package tools
+
+import "strings"
+
+// memoryHintPrefixes are shell commands that read/list/search filesystem content.
+// If these target memory paths, the model should use dedicated memory tools instead.
+var memoryHintPrefixes = []string{
+	"cat ", "head ", "tail ", "less ", "more ",
+	"grep ", "rg ", "ag ",
+	"find ", "ls ", "wc ",
+}
+
+// memoryPathTokens are path fragments indicating memory file access.
+var memoryPathTokens = []string{
+	"MEMORY.md", "memory.md", "memory/",
+}
+
+// MaybeMemoryExecHint checks if a shell command targets memory files
+// (which live in the database, not on disk) and returns an LLM hint.
+// Returns empty string if no memory path detected.
+func MaybeMemoryExecHint(command string) string {
+	trimmed := strings.TrimSpace(command)
+	if trimmed == "" {
+		return ""
+	}
+
+	// Check if command uses a filesystem read/list/search binary.
+	hasReadCmd := false
+	for _, prefix := range memoryHintPrefixes {
+		if strings.HasPrefix(trimmed, prefix) {
+			hasReadCmd = true
+			break
+		}
+	}
+	if !hasReadCmd {
+		return ""
+	}
+
+	// Check if the command references a memory path.
+	for _, token := range memoryPathTokens {
+		if strings.Contains(trimmed, token) {
+			return "[HINT] Memory files are in the database, not on disk. Use memory_search or memory_get tool instead."
+		}
+	}
+
+	return ""
+}
diff --git a/internal/tools/filesystem.go b/internal/tools/filesystem.go
index 7505a2a9..c0e89319 100644
--- a/internal/tools/filesystem.go
+++ b/internal/tools/filesystem.go
@@ -139,7 +139,7 @@ func (t *ReadFileTool) Execute(ctx context.Context, args map[string]any) *Result
 			if content == "" {
 				return SilentResult(fmt.Sprintf("(memory file %s does not exist yet — it will be created when memory is saved)", path))
 			}
-			return SilentResult(content)
+			return SilentResult(content + "\n\n[Source: database, not filesystem]")
 		}
 	}
 
diff --git a/internal/tools/filesystem_list.go b/internal/tools/filesystem_list.go
index 36ebea91..409a7239 100644
--- a/internal/tools/filesystem_list.go
+++ b/internal/tools/filesystem_list.go
@@ -73,7 +73,7 @@ func (t *ListFilesTool) Execute(ctx context.Context, args map[string]any) *Resul
 			if listing == "" {
 				return SilentResult("No memory files stored yet")
 			}
-			return SilentResult(listing)
+			return SilentResult(listing + "\n[Source: database, not filesystem]")
 		}
 	}
 
diff --git a/internal/tools/shell.go b/internal/tools/shell.go
index a843a23b..5d7e1829 100644
--- a/internal/tools/shell.go
+++ b/internal/tools/shell.go
@@ -199,6 +199,11 @@ func (t *ExecTool) Execute(ctx context.Context, args map[string]any) *Result {
 		}
 	}
 
+	// Memory path hint: shell commands can't access DB-backed memory files.
+	if hint := MaybeMemoryExecHint(normalizedCommand); hint != "" {
+		return SilentResult(hint)
+	}
+
 	// Credentialed exec: if command matches a configured binary, use Direct Exec Mode.
 	// This bypasses approval (admin trust) and shell (security).
 	if cred, binary, cmdArgs := t.lookupCredentialedBinary(ctx, command); cred != nil {