diff --git a/apps/desktop/electron/desktop-remote-route.test.ts b/apps/desktop/electron/desktop-remote-route.test.ts
index f68b10d3d6..2a731b77bb 100644
--- a/apps/desktop/electron/desktop-remote-route.test.ts
+++ b/apps/desktop/electron/desktop-remote-route.test.ts
@@ -305,3 +305,90 @@ test('local route does not inherit an unrelated registry SSH connection', () =>
 test('local config without overrides returns null', () => {
   assert.equal(resolveDesktopRemoteRoute({ config: { mode: 'local' }, registry: registry('local', []) }), null)
 })
+
+// --- Registry-primary transport gating (#91564 / #90316) ---
+//
+// "Make primary" on a registered remote gateway only writes connections.json;
+// the v1 config.mode stays 'local'. The route resolver must still expose that
+// remote transport, or startHermes() spawns a loopback `hermes serve` the
+// desktop never uses (duplicated MCP sets, port squat, respawn-on-poll).
+
+test('falls back to a REMOTE registry primary when the v1 mode is local (#91564/#90316)', () => {
+  const route = resolveDesktopRemoteRoute({
+    config: { mode: 'local' },
+    profile: null,
+    registry: registry('gw-b', [
+      { id: 'gw-b', kind: 'remote', label: 'Gateway B', url: 'https://gw-b.test', authMode: 'token', token: tokenB }
+    ])
+  })
+
+  assert.equal(route?.kind, 'remote')
+  assert.equal(route?.source, 'registry')
+  assert.equal(route?.connectionId, 'gw-b')
+  assert.equal((route as any)?.url, 'https://gw-b.test')
+  assert.deepEqual((route as any)?.token, tokenB)
+})
+
+test('falls back to a CLOUD registry primary when the v1 mode is local', () => {
+  const route = resolveDesktopRemoteRoute({
+    config: { mode: 'local' },
+    profile: null,
+    registry: registry('cloud-1', [
+      {
+        id: 'cloud-1',
+        kind: 'cloud',
+        label: 'Hermes Cloud',
+        url: 'https://agent.hermes.cloud',
+        authMode: 'oauth',
+        org: 'nous'
+      }
+    ])
+  })
+
+  assert.equal(route?.kind, 'cloud')
+  assert.equal(route?.source, 'registry')
+  assert.equal((route as any)?.authMode, 'oauth')
+  assert.equal((route as any)?.org, 'nous')
+})
+
+test('falls back to an SSH registry primary when the v1 mode is local', () => {
+  const route = resolveDesktopRemoteRoute({
+    config: { mode: 'local' },
+    profile: null,
+    registry: registry('spark', [
+      { id: 'spark', kind: 'ssh', label: 'Spark', host: 'spark1', user: 'tek', port: 2222, token: tokenA }
+    ])
+  })
+
+  assert.equal(route?.kind, 'ssh')
+  assert.equal(route?.source, 'registry')
+  assert.equal(route?.connectionId, 'spark')
+  assert.equal((route as any)?.ssh?.host, 'spark1')
+  assert.equal((route as any)?.ssh?.port, 2222)
+})
+
+test('a LOCAL registry primary keeps resolving local (null route)', () => {
+  const route = resolveDesktopRemoteRoute({
+    config: { mode: 'local' },
+    profile: null,
+    registry: registry('local', [
+      { id: 'gw-b', kind: 'remote', label: 'Gateway B', url: 'https://gw-b.test', authMode: 'token', token: tokenB }
+    ])
+  })
+
+  assert.equal(route, null)
+})
+
+test('the v1 global remote still outranks the registry primary', () => {
+  const route = resolveDesktopRemoteRoute({
+    config: { mode: 'remote', remote: { url: 'https://global.test', authMode: 'token', token: tokenA } },
+    profile: null,
+    registry: registry('gw-b', [
+      { id: 'global', kind: 'remote', label: 'Global', url: 'https://global.test', token: tokenA },
+      { id: 'gw-b', kind: 'remote', label: 'Gateway B', url: 'https://gw-b.test', authMode: 'token', token: tokenB }
+    ])
+  })
+
+  assert.equal(route?.source, 'settings')
+  assert.equal((route as any)?.url, 'https://global.test')
+})
diff --git a/apps/desktop/electron/desktop-remote-route.ts b/apps/desktop/electron/desktop-remote-route.ts
index c7c8a5cbc6..e41df9b199 100644
--- a/apps/desktop/electron/desktop-remote-route.ts
+++ b/apps/desktop/electron/desktop-remote-route.ts
@@ -9,7 +9,7 @@ import {
 import type { ConnectionRegistry } from './connection-registry'
 import { matchingConnectionId, type StoredRoute } from './connection-route-identity'
 
-type RouteSource = 'env' | 'profile' | 'settings'
+type RouteSource = 'env' | 'profile' | 'registry' | 'settings'
 
 interface SshRouteConfig {
   host: string
@@ -133,7 +133,14 @@ export function resolveDesktopRemoteRoute({
   }
 
   if (!modeIsRemoteLike(config.mode)) {
-    return null
+    // Registry-primary fallback (#91564/#90316): "Make primary" on a
+    // registered remote/cloud/ssh gateway only rewrites connections.json —
+    // the v1 config.mode stays 'local'. Without this rung the primary boot
+    // resolves local and spawns a loopback `hermes serve` the desktop never
+    // uses (it dials the registry primary separately): duplicated MCP sets,
+    // port squat, and a respawn on every poll. A 'local' registry primary
+    // still resolves null, so genuinely-local desktops are untouched.
+    return resolveRegistryPrimaryRoute(registry)
   }
 
   const kind = config.mode === 'cloud' ? 'cloud' : 'remote'
@@ -153,3 +160,53 @@ export function resolveDesktopRemoteRoute({
     matchingConnectionId(registry, route, 'primary')
   )
 }
+
+/**
+ * Lowest-precedence rung: the v2 registry PRIMARY's own transport. Returns
+ * null unless the primary names a remote/cloud/ssh entry — i.e. only when the
+ * user explicitly made a non-local registered gateway their primary.
+ */
+function resolveRegistryPrimaryRoute(registry: ConnectionRegistry): DesktopRemoteRoute | null {
+  const primaryId = String(registry?.primary || '').trim()
+
+  if (!primaryId) {
+    return null
+  }
+
+  const entry = (registry.connections || []).find(connection => connection.id === primaryId)
+
+  if (!entry) {
+    return null
+  }
+
+  if (entry.kind === 'ssh') {
+    const ssh = normalizeSshConfig({ ...entry, mode: 'ssh' })
+
+    if (!ssh) {
+      return null
+    }
+
+    return { connectionId: entry.id, kind: 'ssh', source: 'registry', ssh, token: entry.token }
+  }
+
+  if (entry.kind !== 'remote' && entry.kind !== 'cloud') {
+    return null
+  }
+
+  const url = String(entry.url || '').trim()
+
+  if (!url) {
+    return null
+  }
+
+  return {
+    authMode: normAuthMode(entry.authMode),
+    connectionId: entry.id,
+    headers: entry.headers,
+    kind: entry.kind,
+    org: entry.kind === 'cloud' ? String(entry.org || '').trim() || undefined : undefined,
+    source: 'registry',
+    token: entry.token,
+    url
+  }
+}
diff --git a/apps/desktop/electron/main.ts b/apps/desktop/electron/main.ts
index fcaff6ceb1..a2a0b71f9d 100644
--- a/apps/desktop/electron/main.ts
+++ b/apps/desktop/electron/main.ts
@@ -10092,7 +10092,31 @@ function globalRemoteActive() {
 
   const mode = readDesktopConnectionConfig().mode
 
-  return modeIsRemoteLike(mode) || mode === 'ssh'
+  if (modeIsRemoteLike(mode) || mode === 'ssh') {
+    return true
+  }
+
+  // Registry-primary transport (#91564/#90316): a registered remote/cloud/ssh
+  // gateway promoted to primary via connections.json makes the primary
+  // backend remote even while the v1 config.mode still says 'local'. Every
+  // consumer of this flag ("one remote host serves every profile") must see
+  // that, or the local-entry routes delegate into a primary that now dials
+  // remote — respawning the exact loopback children the resolver rung in
+  // desktop-remote-route.ts eliminates.
+  return registryPrimaryIsRemote()
+}
+
+// True when the v2 registry PRIMARY names a non-local connection. Mirrors the
+// registry fallback rung in resolveDesktopRemoteRoute.
+function registryPrimaryIsRemote() {
+  try {
+    const registry = readDesktopConnectionsRegistry()
+    const entry = registry.connections.find(c => c.id === registry.primary)
+
+    return Boolean(entry && (entry.kind === 'remote' || entry.kind === 'cloud' || entry.kind === 'ssh'))
+  } catch {
+    return false
+  }
 }
 
 // True when the PRIMARY profile's backend resolves to a remote/cloud host —