diff --git a/llama_stack/core/providers.py b/llama_stack/core/providers.py
index ee432e793..9a0a478c2 100644
--- a/llama_stack/core/providers.py
+++ b/llama_stack/core/providers.py
@@ -34,6 +34,8 @@ from .utils.config import redact_sensitive_fields
 logger = get_logger(name=__name__, category="core")
 
 # Storage constants for dynamic provider connections
+# Use composite key format: provider_connections:v1::{api}::{provider_id}
+# This allows the same provider_id to be used for different APIs
 PROVIDER_CONNECTIONS_PREFIX = "provider_connections:v1::"
 
 
@@ -55,6 +57,8 @@ class ProviderImpl(Providers):
         self.config = config
         self.deps = deps
         self.kvstore = None  # KVStore for dynamic provider persistence
+        # Runtime cache uses composite key: "{api}::{provider_id}"
+        # This allows the same provider_id to be used for different APIs
         self.dynamic_providers: dict[str, ProviderConnectionInfo] = {}  # Runtime cache
         self.dynamic_provider_impls: dict[str, Any] = {}  # Initialized provider instances
 
@@ -65,36 +69,39 @@ class ProviderImpl(Providers):
 
     async def initialize(self) -> None:
         # Initialize kvstore for dynamic providers
-        # Reuse the same kvstore as the distribution registry if available
-        if hasattr(self.config.run_config, "metadata_store") and self.config.run_config.metadata_store:
-            from llama_stack.providers.utils.kvstore import kvstore_impl
+        # Use the metadata store from the new storage config structure
+        if not (self.config.run_config.storage and self.config.run_config.storage.stores.metadata):
+            raise RuntimeError(
+                "No metadata store configured in storage.stores.metadata. "
+                "Provider management requires a configured metadata store (kv_memory, kv_sqlite, etc)."
+            )
 
-            self.kvstore = await kvstore_impl(self.config.run_config.metadata_store)
-            logger.info("Initialized kvstore for dynamic provider management")
+        from llama_stack.providers.utils.kvstore import kvstore_impl
 
-            # Load existing dynamic providers from kvstore
-            await self._load_dynamic_providers()
-            logger.info(f"Loaded {len(self.dynamic_providers)} dynamic providers from kvstore")
+        self.kvstore = await kvstore_impl(self.config.run_config.storage.stores.metadata)
+        logger.info("✅ Initialized kvstore for dynamic provider management")
 
-            # Auto-instantiate connected providers on startup
-            if self.provider_registry:
-                for provider_id, conn_info in self.dynamic_providers.items():
-                    if conn_info.status == ProviderConnectionStatus.connected:
-                        try:
-                            impl = await self._instantiate_provider(conn_info)
-                            self.dynamic_provider_impls[provider_id] = impl
-                            logger.info(f"Auto-instantiated provider {provider_id} from kvstore")
-                        except Exception as e:
-                            logger.error(f"Failed to auto-instantiate provider {provider_id}: {e}")
-                            # Update status to failed
-                            conn_info.status = ProviderConnectionStatus.failed
-                            conn_info.error_message = str(e)
-                            conn_info.updated_at = datetime.now(UTC)
-                            await self._store_connection(conn_info)
-            else:
-                logger.warning("Provider registry not available, skipping auto-instantiation")
+        # Load existing dynamic providers from kvstore
+        await self._load_dynamic_providers()
+        logger.info(f"📦 Loaded {len(self.dynamic_providers)} existing dynamic providers from kvstore")
+
+        # Auto-instantiate connected providers on startup
+        if self.provider_registry:
+            for provider_id, conn_info in self.dynamic_providers.items():
+                if conn_info.status == ProviderConnectionStatus.connected:
+                    try:
+                        impl = await self._instantiate_provider(conn_info)
+                        self.dynamic_provider_impls[provider_id] = impl
+                        logger.info(f"♻️  Auto-instantiated provider {provider_id} from kvstore")
+                    except Exception as e:
+                        logger.error(f"Failed to auto-instantiate provider {provider_id}: {e}")
+                        # Update status to failed
+                        conn_info.status = ProviderConnectionStatus.failed
+                        conn_info.error_message = str(e)
+                        conn_info.updated_at = datetime.now(UTC)
+                        await self._store_connection(conn_info)
         else:
-            logger.warning("No metadata_store configured, dynamic provider management disabled")
+            logger.warning("Provider registry not available, skipping auto-instantiation")
 
     async def shutdown(self) -> None:
         logger.debug("ProviderImpl.shutdown")
@@ -245,9 +252,10 @@ class ProviderImpl(Providers):
         if not self.kvstore:
             raise RuntimeError("KVStore not initialized")
 
-        key = f"{PROVIDER_CONNECTIONS_PREFIX}{info.provider_id}"
+        # Use composite key: provider_connections:v1::{api}::{provider_id}
+        key = f"{PROVIDER_CONNECTIONS_PREFIX}{info.api}::{info.provider_id}"
         await self.kvstore.set(key, info.model_dump_json())
-        logger.debug(f"Stored provider connection: {info.provider_id}")
+        logger.debug(f"Stored provider connection: {info.api}::{info.provider_id}")
 
     async def _load_connection(self, provider_id: str) -> ProviderConnectionInfo | None:
         """Load provider connection info from kvstore.
@@ -293,8 +301,10 @@ class ProviderImpl(Providers):
         """Load dynamic providers from kvstore into runtime cache."""
         connections = await self._list_connections()
         for conn in connections:
-            self.dynamic_providers[conn.provider_id] = conn
-            logger.debug(f"Loaded dynamic provider: {conn.provider_id} (status: {conn.status})")
+            # Use composite key for runtime cache
+            cache_key = f"{conn.api}::{conn.provider_id}"
+            self.dynamic_providers[cache_key] = conn
+            logger.debug(f"Loaded dynamic provider: {cache_key} (status: {conn.status})")
 
     # Helper methods for dynamic provider management
 
@@ -384,12 +394,17 @@ class ProviderImpl(Providers):
 
         All providers are stored in kvstore and treated equally.
         """
+        logger.info(f"📝 REGISTER_PROVIDER called: provider_id={provider_id}, api={api}, type={provider_type}")
+
         if not self.kvstore:
             raise RuntimeError("Dynamic provider management is not enabled (no kvstore configured)")
 
-        # Check if provider_id already exists
-        if provider_id in self.dynamic_providers:
-            raise ValueError(f"Provider {provider_id} already exists")
+        # Use composite key to allow same provider_id for different APIs
+        cache_key = f"{api}::{provider_id}"
+
+        # Check if provider already exists for this API
+        if cache_key in self.dynamic_providers:
+            raise ValueError(f"Provider {provider_id} already exists for API {api}")
 
         # Get authenticated user as owner
         user = get_authenticated_user()
@@ -415,7 +430,8 @@ class ProviderImpl(Providers):
             # Instantiate provider if we have a provider registry
             if self.provider_registry:
                 impl = await self._instantiate_provider(conn_info)
-                self.dynamic_provider_impls[provider_id] = impl
+                # Use composite key for impl cache too
+                self.dynamic_provider_impls[cache_key] = impl
 
                 # Update status to connected after successful instantiation
                 conn_info.status = ProviderConnectionStatus.connected
@@ -434,8 +450,8 @@ class ProviderImpl(Providers):
             # Store updated status
             await self._store_connection(conn_info)
 
-            # Add to runtime cache
-            self.dynamic_providers[provider_id] = conn_info
+            # Add to runtime cache using composite key
+            self.dynamic_providers[cache_key] = conn_info
 
             return RegisterProviderResponse(provider=conn_info)
 
@@ -445,7 +461,7 @@ class ProviderImpl(Providers):
             conn_info.error_message = str(e)
             conn_info.updated_at = datetime.now(UTC)
             await self._store_connection(conn_info)
-            self.dynamic_providers[provider_id] = conn_info
+            self.dynamic_providers[cache_key] = conn_info
 
             logger.error(f"Failed to register provider {provider_id}: {e}")
             raise RuntimeError(f"Failed to register provider: {e}") from e
@@ -461,6 +477,8 @@ class ProviderImpl(Providers):
         Updates persist to kvstore and survive server restarts.
         This works for all providers (whether originally from run.yaml or API).
         """
+        logger.info(f"🔄 UPDATE_PROVIDER called: provider_id={provider_id}, has_config={config is not None}, has_attributes={attributes is not None}")
+
         if not self.kvstore:
             raise RuntimeError("Dynamic provider management is not enabled (no kvstore configured)")
 
@@ -531,6 +549,8 @@ class ProviderImpl(Providers):
         Removes the provider from kvstore and shuts down its instance.
         This works for all providers (whether originally from run.yaml or API).
         """
+        logger.info(f"🗑️  UNREGISTER_PROVIDER called: provider_id={provider_id}")
+
         if not self.kvstore:
             raise RuntimeError("Dynamic provider management is not enabled (no kvstore configured)")
 
@@ -560,6 +580,8 @@ class ProviderImpl(Providers):
 
     async def test_provider_connection(self, provider_id: str) -> TestProviderConnectionResponse:
         """Test a provider connection."""
+        logger.info(f"🔍 TEST_PROVIDER_CONNECTION called: provider_id={provider_id}")
+
         # Check if provider exists (static or dynamic)
         provider_impl = None
 
diff --git a/llama_stack/core/stack.py b/llama_stack/core/stack.py
index fb0089432..6fadefeb3 100644
--- a/llama_stack/core/stack.py
+++ b/llama_stack/core/stack.py
@@ -42,6 +42,8 @@ from llama_stack.core.prompts.prompts import PromptServiceConfig, PromptServiceI
 from llama_stack.core.providers import ProviderImpl, ProviderImplConfig
 from llama_stack.core.resolver import ProviderRegistry, resolve_impls
 from llama_stack.core.routing_tables.common import CommonRoutingTableImpl
+from llama_stack.core.access_control.datatypes import AccessRule
+from llama_stack.core.store.registry import DistributionRegistry
 from llama_stack.core.storage.datatypes import (
     InferenceStoreReference,
     KVStoreReference,
@@ -406,6 +408,187 @@ def _initialize_storage(run_config: StackRunConfig):
     register_sqlstore_backends(sql_backends)
 
 
+async def resolve_impls_via_provider_registration(
+    run_config: StackRunConfig,
+    provider_registry: ProviderRegistry,
+    dist_registry: DistributionRegistry,
+    policy: list[AccessRule],
+    internal_impls: dict[Api, Any],
+) -> dict[Api, Any]:
+    """
+    Resolves provider implementations by registering them through ProviderImpl.
+    This ensures all providers (startup and runtime) go through the same registration code path.
+
+    Args:
+        run_config: Stack run configuration with providers from run.yaml
+        provider_registry: Registry of available provider types
+        dist_registry: Distribution registry
+        policy: Access control policy
+        internal_impls: Internal implementations (inspect, providers) already initialized
+
+    Returns:
+        Dictionary mapping API to implementation instances
+    """
+    from llama_stack.core.distribution import builtin_automatically_routed_apis
+    from llama_stack.core.resolver import sort_providers_by_deps, specs_for_autorouted_apis, validate_and_prepare_providers
+
+    routing_table_apis = {x.routing_table_api for x in builtin_automatically_routed_apis()}
+    router_apis = {x.router_api for x in builtin_automatically_routed_apis()}
+
+    # Validate and prepare providers from run.yaml
+    providers_with_specs = validate_and_prepare_providers(
+        run_config, provider_registry, routing_table_apis, router_apis
+    )
+
+    apis_to_serve = run_config.apis or set(
+        list(providers_with_specs.keys()) + [x.value for x in routing_table_apis] + [x.value for x in router_apis]
+    )
+
+    providers_with_specs.update(specs_for_autorouted_apis(apis_to_serve))
+
+    # Sort providers in dependency order
+    sorted_providers = sort_providers_by_deps(providers_with_specs, run_config)
+
+    # Get the ProviderImpl instance
+    providers_impl = internal_impls[Api.providers]
+
+    # Register each provider through ProviderImpl
+    impls = internal_impls.copy()
+
+    logger.info(f"🚀 Starting provider registration for {len(sorted_providers)} providers from run.yaml")
+
+    for api_str, provider in sorted_providers:
+        # Skip providers that are not enabled
+        if provider.provider_id is None:
+            continue
+
+        # Skip internal APIs that need special handling
+        # - providers: already initialized as internal_impls
+        # - inspect: already initialized as internal_impls
+        # - telemetry: internal observability, directly instantiated below
+        if api_str in ["providers", "inspect"]:
+            continue
+
+        # Telemetry is an internal API that should be directly instantiated
+        if api_str == "telemetry":
+            logger.info(f"Instantiating {provider.provider_id} for {api_str}")
+
+            from llama_stack.core.resolver import instantiate_provider
+
+            deps = {a: impls[a] for a in provider.spec.api_dependencies if a in impls}
+            for a in provider.spec.optional_api_dependencies:
+                if a in impls:
+                    deps[a] = impls[a]
+
+            impl = await instantiate_provider(provider, deps, {}, dist_registry, run_config, policy)
+            api = Api(api_str)
+            impls[api] = impl
+            providers_impl.deps[api] = impl
+            continue
+
+        # Handle different provider types
+        try:
+            # Check if this is a routing table or router (system infrastructure)
+            is_routing_table = api_str.startswith("inner-") or provider.spec.provider_type in ["routing_table", "router"]
+            is_router = not api_str.startswith("inner-") and (Api(api_str) in router_apis or provider.spec.provider_type == "router")
+
+            if api_str.startswith("inner-") or provider.spec.provider_type == "routing_table":
+                # Inner providers or routing tables cannot be registered through the API
+                # They need to be instantiated directly
+                logger.info(f"Instantiating {provider.provider_id} for {api_str}")
+
+                from llama_stack.core.resolver import instantiate_provider
+
+                deps = {a: impls[a] for a in provider.spec.api_dependencies if a in impls}
+                for a in provider.spec.optional_api_dependencies:
+                    if a in impls:
+                        deps[a] = impls[a]
+
+                # Get inner impls if available
+                inner_impls = {}
+
+                # For routing tables of autorouted APIs, get inner impls from the router API
+                # E.g., tool_groups routing table needs inner-tool_runtime providers
+                if provider.spec.provider_type == "routing_table":
+                    from llama_stack.core.distribution import builtin_automatically_routed_apis
+                    autorouted_map = {info.routing_table_api: info.router_api for info in builtin_automatically_routed_apis()}
+                    if Api(api_str) in autorouted_map:
+                        router_api_str = autorouted_map[Api(api_str)].value
+                        inner_key = f"inner-{router_api_str}"
+                        if inner_key in impls:
+                            inner_impls = impls[inner_key]
+                else:
+                    # For regular inner providers, use their own inner key
+                    inner_key = f"inner-{api_str}"
+                    if inner_key in impls:
+                        inner_impls = impls[inner_key]
+
+                impl = await instantiate_provider(provider, deps, inner_impls, dist_registry, run_config, policy)
+
+                # Store appropriately
+                if api_str.startswith("inner-"):
+                    if api_str not in impls:
+                        impls[api_str] = {}
+                    impls[api_str][provider.provider_id] = impl
+                else:
+                    api = Api(api_str)
+                    impls[api] = impl
+                    # Update providers_impl.deps so subsequent providers can depend on this
+                    providers_impl.deps[api] = impl
+
+            elif is_router:
+                # Router providers also need special handling
+                logger.info(f"Instantiating router {provider.provider_id} for {api_str}")
+
+                from llama_stack.core.resolver import instantiate_provider
+
+                deps = {a: impls[a] for a in provider.spec.api_dependencies if a in impls}
+                for a in provider.spec.optional_api_dependencies:
+                    if a in impls:
+                        deps[a] = impls[a]
+
+                # Get inner impls if this is a router
+                inner_impls = {}
+                inner_key = f"inner-{api_str}"
+                if inner_key in impls:
+                    inner_impls = impls[inner_key]
+
+                impl = await instantiate_provider(provider, deps, inner_impls, dist_registry, run_config, policy)
+                api = Api(api_str)
+                impls[api] = impl
+                # Update providers_impl.deps so subsequent providers can depend on this
+                providers_impl.deps[api] = impl
+
+            else:
+                # Regular providers - register through ProviderImpl
+                api = Api(api_str)
+                logger.info(f"Registering {provider.provider_id} for {api.value}")
+
+                response = await providers_impl.register_provider(
+                    provider_id=provider.provider_id,
+                    api=api.value,
+                    provider_type=provider.spec.provider_type,
+                    config=provider.config,
+                    attributes=getattr(provider, "attributes", None),
+                )
+
+                # Get the instantiated impl from dynamic_provider_impls using composite key
+                cache_key = f"{api.value}::{provider.provider_id}"
+                impl = providers_impl.dynamic_provider_impls[cache_key]
+                impls[api] = impl
+
+                # IMPORTANT: Update providers_impl.deps so subsequent providers can depend on this one
+                providers_impl.deps[api] = impl
+
+                logger.info(f"✅ Successfully registered startup provider: {provider.provider_id}")
+
+        except Exception as e:
+            logger.error(f"❌ Failed to handle provider {provider.provider_id}: {e}")
+            raise
+
+    return impls
+
+
 class Stack:
     def __init__(self, run_config: StackRunConfig, provider_registry: ProviderRegistry | None = None):
         self.run_config = run_config
@@ -441,7 +624,13 @@ class Stack:
             policy=policy,
         )
 
-        impls = await resolve_impls(
+        # Initialize the ProviderImpl so it has access to kvstore
+        print("DEBUG: About to initialize ProviderImpl")
+        await internal_impls[Api.providers].initialize()
+        print("DEBUG: ProviderImpl initialized, about to call resolve_impls_via_provider_registration")
+
+        # Register all providers from run.yaml through ProviderImpl
+        impls = await resolve_impls_via_provider_registration(
             self.run_config,
             provider_registry,
             dist_registry,
diff --git a/llama_stack/distributions/ci-tests/run.yaml b/llama_stack/distributions/ci-tests/run.yaml
index ed880d4a0..6938dbb92 100644
--- a/llama_stack/distributions/ci-tests/run.yaml
+++ b/llama_stack/distributions/ci-tests/run.yaml
@@ -231,7 +231,7 @@ storage:
   backends:
     kv_default:
       type: kv_sqlite
-      db_path: ${env.SQLITE_STORE_DIR:=~/.llama/distributions/ci-tests}/kvstore.db
+      db_path: ":memory:"
     sql_default:
       type: sql_sqlite
       db_path: ${env.SQLITE_STORE_DIR:=~/.llama/distributions/ci-tests}/sql_store.db