diff --git a/internal/install/clients.go b/internal/install/clients.go
index 67b8859..b8a1be1 100644
--- a/internal/install/clients.go
+++ b/internal/install/clients.go
@@ -50,6 +50,16 @@ func (c Client) InstallCmdDisplay(binPath string) string {
 	return strings.Join(out, " ")
 }
 
+// CLIOnPath reports whether the client's CLI binary resolves via PATH.
+// Pure-config clients (empty CLIProbe) are treated as callable.
+func (c Client) CLIOnPath() bool {
+	if c.CLIProbe == "" {
+		return true
+	}
+	_, err := exec.LookPath(c.CLIProbe)
+	return err == nil
+}
+
 // Detected returns true if this client appears installed on the system.
 // Check order: CLI on PATH → config file exists.
 func (c Client) Detected() bool {
@@ -70,6 +80,19 @@ func (c Client) Detected() bool {
 	return false
 }
 
+// partitionCallableClients splits detected clients into those whose CLI is on
+// PATH (callable) and those detected only via a config-file probe (skipped).
+func partitionCallableClients(clients []Client) (callable, skipped []Client) {
+	for _, c := range clients {
+		if c.CLIOnPath() {
+			callable = append(callable, c)
+		} else {
+			skipped = append(skipped, c)
+		}
+	}
+	return callable, skipped
+}
+
 // Clients is the supported-client registry. Adding a new client means
 // adding a struct literal here and (optionally) a unit test.
 var Clients = []Client{
diff --git a/internal/install/init.go b/internal/install/init.go
index 88a9560..8077329 100644
--- a/internal/install/init.go
+++ b/internal/install/init.go
@@ -145,16 +145,17 @@ func Init(ctx context.Context, repoRoot string, opts InitOptions) (*InitResult,
 
 	// Detect which MCP host(s) are present. opts.clients lets tests
 	// inject a fake set without running real detection.
-	var detected []Client
+	var allDetected []Client
 	if opts.clients != nil {
 		for _, c := range opts.clients {
 			if c.Detected() {
-				detected = append(detected, c)
+				allDetected = append(allDetected, c)
 			}
 		}
 	} else {
-		detected = detectHosts()
+		allDetected = detectHosts()
 	}
+	callableClients, skippedMissingCLI := partitionCallableClients(allDetected)
 	binPath := "guild"
 	if exe, err := resolveAbsBinPath(os.Executable); err == nil {
 		binPath = exe
@@ -178,11 +179,15 @@ func Init(ctx context.Context, repoRoot string, opts InitOptions) (*InitResult,
 	case agentsSkip:
 		fmt.Fprintln(opts.Out, "  [✓] AGENTS.md — guild section up-to-date → skip")
 	}
-	if len(detected) > 0 {
-		for _, c := range detected {
+	if len(allDetected) > 0 {
+		for _, c := range callableClients {
 			fmt.Fprintf(opts.Out, "  [?] register guild MCP — detected: %s\n        command: %s\n",
 				c.Name, c.InstallCmdDisplay(binPath))
 		}
+		for _, c := range skippedMissingCLI {
+			fmt.Fprintf(opts.Out, "  [i] register guild MCP — skipping %s: %s not on PATH\n",
+				c.Name, c.CLIProbe)
+		}
 	} else {
 		fmt.Fprintln(opts.Out, "  [?] register guild MCP — no host detected; see `guild mcp install` for options")
 	}
@@ -293,7 +298,7 @@ func Init(ctx context.Context, repoRoot string, opts InitOptions) (*InitResult,
 	// Delegate to MCPInstall with Run: true so each detected client gets a
 	// per-client [Y/n] confirm and the registration command actually executes.
 	// No-client path keeps the manual-setup hint.
-	if len(detected) > 0 {
+	if len(callableClients) > 0 {
 		fmt.Fprintln(opts.Out)
 		execFn := opts.executableFn
 		if execFn == nil {
@@ -304,14 +309,14 @@ func Init(ctx context.Context, repoRoot string, opts InitOptions) (*InitResult,
 			Yes:          opts.Yes,
 			Out:          opts.Out,
 			In:           opts.In,
-			clients:      detected,
+			clients:      callableClients,
 			executableFn: execFn,
 			execCmdFn:    opts.execCmdFn,
 		}
 		if _, err := MCPInstall(ctx, mcpOpts); err != nil {
 			return nil, fmt.Errorf("install: mcp register: %w", err)
 		}
-	} else {
+	} else if len(allDetected) == 0 {
 		fmt.Fprintln(opts.Out)
 		fmt.Fprintln(opts.Out, "  [i] no MCP client detected — see `guild mcp install` for manual setup")
 	}
diff --git a/internal/install/init_test.go b/internal/install/init_test.go
index f8fdd01..ee58238 100644
--- a/internal/install/init_test.go
+++ b/internal/install/init_test.go
@@ -10,6 +10,29 @@ import (
 	"testing"
 )
 
+// configOnlyClient builds a Client detected via its config probe but whose
+// CLI binary is absent from PATH. Used to exercise issue #90.
+func configOnlyClient(t *testing.T, name, cliProbe, configRelPath string) Client {
+	t.Helper()
+	home := t.TempDir()
+	configPath := filepath.Join(home, strings.TrimPrefix(configRelPath, "~/"))
+	if err := os.MkdirAll(filepath.Dir(configPath), 0o755); err != nil {
+		t.Fatalf("mkdir config dir: %v", err)
+	}
+	if err := os.WriteFile(configPath, []byte("{}"), 0o644); err != nil {
+		t.Fatalf("write config probe: %v", err)
+	}
+	t.Setenv("HOME", home)
+	return Client{
+		Name:        name,
+		CLIProbe:    cliProbe,
+		ConfigProbe: configRelPath,
+		InstallArgv: func(binPath string) []string {
+			return []string{cliProbe, "mcp", "add", "guild", "--", binPath, "mcp", "serve"}
+		},
+	}
+}
+
 // fakeClient builds a Client that always reports Detected()=true by pointing
 // CLIProbe at a real executable on PATH. Paired with an injected execCmdFn,
 // lets tests observe the MCP registration path without running real CLI.
@@ -566,3 +589,40 @@ func TestInit_MCPRegistration_NoClient_PrintsHint(t *testing.T) {
 		t.Errorf("expected manual-setup hint; got:\n%s", out.String())
 	}
 }
+
+// Config-detected client without CLI on PATH must be skipped in the init
+// plan and must not invoke registration (issue #90).
+func TestInit_MCPRegistration_SkipsConfigOnlyClientWithoutCLI(t *testing.T) {
+	ctx := context.Background()
+	dir := makeRepo(t, "skipmcp")
+	loreDB, questDB := testDBPaths(t)
+	var out bytes.Buffer
+	var calls [][]string
+
+	missingCLI := "nonexistent-init-cli-xyzzy-99"
+	client := configOnlyClient(t, "Cursor", missingCLI, "~/.cursor/mcp.json")
+
+	_, err := Init(ctx, dir, InitOptions{
+		Yes:          true,
+		Out:          &out,
+		In:           &bytes.Buffer{},
+		LoreDBPath:   loreDB,
+		QuestDBPath:  questDB,
+		clients:      []Client{client},
+		execCmdFn:    recordingExec(&calls),
+		executableFn: fakeExecutable(t),
+	})
+	if err != nil {
+		t.Fatalf("Init: %v", err)
+	}
+	output := out.String()
+	if !strings.Contains(output, "skipping Cursor: "+missingCLI+" not on PATH") {
+		t.Errorf("expected skip notice in plan; got:\n%s", output)
+	}
+	if strings.Contains(output, "no MCP client detected") {
+		t.Errorf("should not print no-client hint when client was detected but skipped:\n%s", output)
+	}
+	if len(calls) != 0 {
+		t.Errorf("registration must not run when CLI missing, got %d calls: %+v", len(calls), calls)
+	}
+}