diff --git a/CLAUDE.md b/CLAUDE.md
index 0febb72..5a4b220 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -241,7 +241,7 @@ Returns backend server status for a specific domain:
 
 **Status values:** `healthy` (all UP), `degraded` (partial UP), `down` (all DOWN), `no_servers`
 
-## MCP Tools (28 total)
+## MCP Tools (29 total)
 
 ### Domain Management
 | Tool | Description |
@@ -285,7 +285,7 @@ Returns backend server status for a specific domain:
 | `haproxy_save_state` | Save server state to disk (legacy) |
 | `haproxy_restore_state` | Restore state from disk (legacy) |
 
-### Certificate Management
+### Certificate Management (Zero-Downtime via Runtime API)
 | Tool | Description |
 |------|-------------|
 | `haproxy_list_certs` | List all certificates with expiry info |
@@ -294,6 +294,7 @@ Returns backend server status for a specific domain:
 | `haproxy_renew_cert` | Renew specific certificate (force option available) |
 | `haproxy_renew_all_certs` | Renew all certificates due for renewal |
 | `haproxy_delete_cert` | Delete certificate from acme.sh and HAProxy |
+| `haproxy_load_cert` | Load/reload certificate into HAProxy (manual trigger) |
 
 ## Key Conventions
 
@@ -335,6 +336,13 @@ api.example.com → pool_6
   - Startup restore: All servers restored in 1 connection (was 2×N for N servers)
   - Example: 7 servers restored = 1 connection (was 14 connections)
 
+### Zero-Downtime Certificate Management
+- **Runtime API**: Certificates loaded/updated without HAProxy reload
+  - `new ssl cert` → `set ssl cert` → `commit ssl cert`
+  - No connection drops during certificate changes
+- **Persistence**: `certificates.json` stores domain list
+- **Auto-restore**: Certificates reloaded into HAProxy on MCP startup
+
 ## HAProxy Runtime API
 
 ```bash
@@ -369,17 +377,18 @@ echo "set server pool_1/pool_1_1 state ready" | nc localhost 9999
 │   ├── haproxy_client.py # HAProxy Runtime API client
 │   ├── file_ops.py      # File I/O operations
 │   ├── utils.py         # Parsing utilities
-│   └── tools/           # MCP tools (28 total)
+│   └── tools/           # MCP tools (29 total)
 │       ├── domains.py   # Domain management (3 tools)
 │       ├── servers.py   # Server management (7 tools)
 │       ├── health.py    # Health checks (3 tools)
 │       ├── monitoring.py # Monitoring (4 tools)
 │       ├── configuration.py # Config management (4 tools)
-│       └── certificates.py # Certificate management (6 tools)
+│       └── certificates.py # Certificate management (7 tools)
 ├── conf/
 │   ├── haproxy.cfg      # Main HAProxy config (100 pool backends)
 │   ├── domains.map      # Domain → Pool mapping
 │   ├── servers.json     # Server persistence (auto-managed)
+│   ├── certificates.json # Certificate domain list (auto-managed)
 │   └── mcp-token.env    # Bearer token for MCP auth
 ├── certs/               # SSL/TLS certificates (HAProxy PEM format)
 ├── data/                # Legacy state files
@@ -419,9 +428,11 @@ echo "set server pool_1/pool_1_1 state ready" | nc localhost 9999
    ↓
 4. systemd starts haproxy-mcp.service
    ↓
-5. MCP server reads servers.json
+5. MCP server reads servers.json & certificates.json
    ↓
 6. MCP server restores servers via Runtime API
    ↓
-7. Ready to serve traffic
+7. MCP server loads certificates via Runtime API (zero-downtime)
+   ↓
+8. Ready to serve traffic
 ```
diff --git a/conf/certificates.json b/conf/certificates.json
new file mode 100644
index 0000000..4215184
--- /dev/null
+++ b/conf/certificates.json
@@ -0,0 +1,7 @@
+{
+  "domains": [
+    "actions.it.com",
+    "anvil.it.com",
+    "inouter.com"
+  ]
+}
diff --git a/haproxy_mcp/tools/certificates.py b/haproxy_mcp/tools/certificates.py
index e438dd2..31541f7 100644
--- a/haproxy_mcp/tools/certificates.py
+++ b/haproxy_mcp/tools/certificates.py
@@ -1,5 +1,6 @@
 """Certificate management tools for HAProxy MCP Server."""
 
+import json
 import os
 import subprocess
 from datetime import datetime
@@ -7,18 +8,161 @@ from typing import Annotated
 
 from pydantic import Field
 
-from ..config import logger, SUBPROCESS_TIMEOUT, HAPROXY_CONTAINER
+from ..config import logger, SUBPROCESS_TIMEOUT
 from ..validation import validate_domain
+from ..haproxy_client import haproxy_cmd
+from ..file_ops import atomic_write_file
 
 # Certificate paths
 ACME_SH = os.path.expanduser("~/.acme.sh/acme.sh")
 ACME_HOME = os.path.expanduser("~/.acme.sh")
 CERTS_DIR = "/opt/haproxy/certs"
+CERTS_DIR_CONTAINER = "/etc/haproxy/certs"
+CERTS_JSON = "/opt/haproxy/conf/certificates.json"
 
 # Longer timeout for certificate operations (ACME can be slow)
 CERT_TIMEOUT = 120
 
 
+def get_pem_paths(domain: str) -> tuple[str, str]:
+    """Get host and container PEM paths for a domain.
+
+    Args:
+        domain: Domain name
+
+    Returns:
+        Tuple of (host_path, container_path)
+    """
+    return (
+        os.path.join(CERTS_DIR, f"{domain}.pem"),
+        os.path.join(CERTS_DIR_CONTAINER, f"{domain}.pem")
+    )
+
+
+def load_cert_config() -> list[str]:
+    """Load certificate domain list from JSON file.
+
+    Returns:
+        List of domain names
+    """
+    try:
+        with open(CERTS_JSON, "r", encoding="utf-8") as f:
+            data = json.load(f)
+            return data.get("domains", [])
+    except FileNotFoundError:
+        return []
+    except json.JSONDecodeError as e:
+        logger.warning("Corrupt certificates.json: %s", e)
+        return []
+
+
+def save_cert_config(domains: list[str]) -> None:
+    """Save certificate domain list to JSON file atomically.
+
+    Args:
+        domains: List of domain names
+    """
+    atomic_write_file(CERTS_JSON, json.dumps({"domains": sorted(domains)}, indent=2))
+
+
+def add_cert_to_config(domain: str) -> None:
+    """Add a domain to the certificate config."""
+    domains = load_cert_config()
+    if domain not in domains:
+        domains.append(domain)
+        save_cert_config(domains)
+
+
+def remove_cert_from_config(domain: str) -> None:
+    """Remove a domain from the certificate config."""
+    domains = load_cert_config()
+    if domain in domains:
+        domains.remove(domain)
+        save_cert_config(domains)
+
+
+def load_cert_to_haproxy(domain: str) -> tuple[bool, str]:
+    """Load a certificate into HAProxy via Runtime API (zero-downtime).
+
+    Args:
+        domain: Domain name
+
+    Returns:
+        Tuple of (success, message)
+    """
+    host_path, container_path = get_pem_paths(domain)
+
+    if not os.path.exists(host_path):
+        return False, f"PEM file not found: {host_path}"
+
+    try:
+        # Read PEM content
+        with open(host_path, "r", encoding="utf-8") as f:
+            pem_content = f.read()
+
+        # Check if cert already loaded
+        result = haproxy_cmd("show ssl cert")
+        if container_path in result:
+            # Update existing cert
+            haproxy_cmd(f"set ssl cert {container_path} <<\n{pem_content}\n")
+            haproxy_cmd(f"commit ssl cert {container_path}")
+            return True, "updated"
+        else:
+            # Add new cert
+            haproxy_cmd(f"new ssl cert {container_path}")
+            haproxy_cmd(f"set ssl cert {container_path} <<\n{pem_content}\n")
+            haproxy_cmd(f"commit ssl cert {container_path}")
+            return True, "added"
+
+    except Exception as e:
+        return False, str(e)
+
+
+def unload_cert_from_haproxy(domain: str) -> tuple[bool, str]:
+    """Unload a certificate from HAProxy via Runtime API.
+
+    Args:
+        domain: Domain name
+
+    Returns:
+        Tuple of (success, message)
+    """
+    _, container_path = get_pem_paths(domain)
+
+    try:
+        # Check if cert is loaded
+        result = haproxy_cmd("show ssl cert")
+        if container_path not in result:
+            return True, "not loaded"
+
+        # Delete from HAProxy runtime
+        haproxy_cmd(f"del ssl cert {container_path}")
+        return True, "unloaded"
+
+    except Exception as e:
+        return False, str(e)
+
+
+def restore_certificates() -> int:
+    """Restore all certificates from config to HAProxy on startup.
+
+    Returns:
+        Number of certificates restored
+    """
+    domains = load_cert_config()
+    restored = 0
+
+    for domain in domains:
+        success, msg = load_cert_to_haproxy(domain)
+        if success:
+            restored += 1
+            logger.debug("Certificate %s: %s", domain, msg)
+        else:
+            logger.warning("Failed to restore certificate %s: %s", domain, msg)
+
+    return restored
+
+
 def register_certificate_tools(mcp):
     """Register certificate management tools with MCP server."""
 
@@ -42,19 +186,23 @@ def register_certificate_tools(mcp):
             if len(lines) <= 1:
                 return "No certificates found"
 
+            # Get HAProxy loaded certs
+            try:
+                haproxy_certs = haproxy_cmd("show ssl cert")
+            except Exception:
+                haproxy_certs = ""
+
             # Parse and format output
-            # Format: Main_Domain KeyLength SAN_Domains Profile CA Created Renew
             certs = []
             for line in lines[1:]:  # Skip header
                 parts = line.split()
                 if len(parts) >= 4:
                     domain = parts[0]
-                    # Find CA and dates by looking for known patterns
                     ca = "unknown"
                     created = "unknown"
                     renew = "unknown"
 
-                    for i, part in enumerate(parts):
+                    for part in parts:
                         if "Google" in part or "LetsEncrypt" in part or "ZeroSSL" in part:
                             ca = part
                         elif part.endswith("Z") and "T" in part:
@@ -63,11 +211,16 @@ def register_certificate_tools(mcp):
                             else:
                                 renew = part
 
-                    # Check if PEM exists in HAProxy certs dir
-                    pem_path = os.path.join(CERTS_DIR, f"{domain}.pem")
-                    deployed = "deployed" if os.path.exists(pem_path) else "not deployed"
+                    # Check deployment status
+                    host_path, container_path = get_pem_paths(domain)
+                    if container_path in haproxy_certs:
+                        status = "loaded"
+                    elif os.path.exists(host_path):
+                        status = "file exists (not loaded)"
+                    else:
+                        status = "not deployed"
 
-                    certs.append(f"• {domain} ({ca})\n  Created: {created}\n  Renew: {renew}\n  Status: {deployed}")
+                    certs.append(f"• {domain} ({ca})\n  Created: {created}\n  Renew: {renew}\n  Status: {status}")
 
             return "\n\n".join(certs) if certs else "No certificates found"
         except subprocess.TimeoutExpired:
@@ -88,14 +241,14 @@ def register_certificate_tools(mcp):
         if not validate_domain(domain):
             return "Error: Invalid domain format"
 
-        pem_path = os.path.join(CERTS_DIR, f"{domain}.pem")
-        if not os.path.exists(pem_path):
+        host_path, container_path = get_pem_paths(domain)
+        if not os.path.exists(host_path):
             return f"Error: Certificate not found for {domain}"
 
         try:
             # Use openssl to get certificate info
             result = subprocess.run(
-                ["openssl", "x509", "-in", pem_path, "-noout",
+                ["openssl", "x509", "-in", host_path, "-noout",
                  "-subject", "-issuer", "-dates", "-ext", "subjectAltName"],
                 capture_output=True, text=True, timeout=SUBPROCESS_TIMEOUT
             )
@@ -103,13 +256,21 @@ def register_certificate_tools(mcp):
                 return f"Error reading certificate: {result.stderr}"
 
             # Get file info
-            stat = os.stat(pem_path)
+            stat = os.stat(host_path)
             modified = datetime.fromtimestamp(stat.st_mtime).strftime("%Y-%m-%d %H:%M:%S")
 
+            # Check HAProxy status
+            try:
+                haproxy_certs = haproxy_cmd("show ssl cert")
+                loaded = "Yes" if container_path in haproxy_certs else "No"
+            except Exception:
+                loaded = "Unknown"
+
             info = [
                 f"Certificate: {domain}",
-                f"File: {pem_path}",
+                f"File: {host_path}",
                 f"Modified: {modified}",
+                f"Loaded in HAProxy: {loaded}",
                 "---",
                 result.stdout.strip()
             ]
@@ -126,7 +287,7 @@ def register_certificate_tools(mcp):
     ) -> str:
         """Issue a new SSL/TLS certificate using acme.sh with Cloudflare DNS.
 
-        Automatically deploys to HAProxy after issuance.
+        Automatically deploys to HAProxy via Runtime API (zero-downtime).
 
         Example: haproxy_issue_cert("example.com", wildcard=True)
         """
@@ -135,7 +296,6 @@ def register_certificate_tools(mcp):
 
         # Check if CF_Token is available
         if not os.environ.get("CF_Token"):
-            # Try to load from secrets file
             secrets_file = os.path.expanduser("~/.secrets/cloudflare.ini")
             if os.path.exists(secrets_file):
                 try:
@@ -156,9 +316,11 @@ def register_certificate_tools(mcp):
         if os.path.exists(cert_dir):
             return f"Error: Certificate for {domain} already exists. Use haproxy_renew_cert to renew."
 
-        # Build acme.sh command
-        pem_path = os.path.join(CERTS_DIR, f"{domain}.pem")
-        reload_cmd = f"cat {ACME_HOME}/{domain}_ecc/fullchain.cer {ACME_HOME}/{domain}_ecc/{domain}.key > {pem_path} && podman exec {HAPROXY_CONTAINER} kill -USR2 1"
+        # Build acme.sh command (without reload - we'll do it via Runtime API)
+        host_path, _ = get_pem_paths(domain)
+
+        # Create PEM after issuance
+        install_cmd = f"cat {ACME_HOME}/{domain}_ecc/fullchain.cer {ACME_HOME}/{domain}_ecc/{domain}.key > {host_path}"
 
         cmd = [
             ACME_SH, "--issue",
@@ -169,7 +331,7 @@ def register_certificate_tools(mcp):
         if wildcard:
             cmd.extend(["-d", f"*.{domain}"])
 
-        cmd.extend(["--reloadcmd", reload_cmd])
+        cmd.extend(["--reloadcmd", install_cmd])
 
         try:
             logger.info("Issuing certificate for %s", domain)
@@ -183,11 +345,17 @@ def register_certificate_tools(mcp):
                 error_msg = result.stderr or result.stdout
                 return f"Error issuing certificate:\n{error_msg}"
 
-            # Verify deployment
-            if os.path.exists(pem_path):
-                return f"Certificate issued and deployed for {domain}\nFile: {pem_path}"
+            # Load into HAProxy via Runtime API (zero-downtime)
+            if os.path.exists(host_path):
+                success, msg = load_cert_to_haproxy(domain)
+                if success:
+                    # Save to config for persistence
+                    add_cert_to_config(domain)
+                    return f"Certificate issued and loaded for {domain} ({msg})"
+                else:
+                    return f"Certificate issued but HAProxy loading failed: {msg}"
             else:
-                return f"Certificate issued but deployment may have failed. Check {pem_path}"
+                return f"Certificate issued but PEM file not created. Check {host_path}"
 
         except subprocess.TimeoutExpired:
             return f"Error: Certificate issuance timed out after {CERT_TIMEOUT}s"
@@ -201,6 +369,8 @@ def register_certificate_tools(mcp):
     ) -> str:
         """Renew an existing certificate.
 
+        Uses Runtime API for zero-downtime reload.
+
         Example: haproxy_renew_cert("example.com", force=True)
         """
         if not validate_domain(domain):
@@ -224,14 +394,20 @@ def register_certificate_tools(mcp):
 
             output = result.stdout + result.stderr
 
-            if "Cert success" in output or "Reload success" in output:
-                return f"Certificate renewed for {domain}"
-            elif "Skip" in output and "Not in renewal period" in output:
+            if "Skip" in output and "Not yet due" in output:
                 return f"Certificate for {domain} not due for renewal. Use force=True to force renewal."
-            elif result.returncode != 0:
-                return f"Error renewing certificate:\n{output}"
+
+            if "Cert success" in output or result.returncode == 0:
+                # Reload into HAProxy via Runtime API
+                success, msg = load_cert_to_haproxy(domain)
+                if success:
+                    # Ensure in config
+                    add_cert_to_config(domain)
+                    return f"Certificate renewed and reloaded for {domain} ({msg})"
+                else:
+                    return f"Certificate renewed but HAProxy reload failed: {msg}"
             else:
-                return f"Renewal completed:\n{output}"
+                return f"Error renewing certificate:\n{output}"
 
         except subprocess.TimeoutExpired:
             return f"Error: Certificate renewal timed out after {CERT_TIMEOUT}s"
@@ -248,7 +424,7 @@ def register_certificate_tools(mcp):
             logger.info("Running certificate renewal cron")
             result = subprocess.run(
                 [ACME_SH, "--cron"],
-                capture_output=True, text=True, timeout=CERT_TIMEOUT * 3,  # Longer timeout for all certs
+                capture_output=True, text=True, timeout=CERT_TIMEOUT * 3,
                 env={**os.environ, "HOME": os.path.expanduser("~")}
             )
 
@@ -258,8 +434,15 @@ def register_certificate_tools(mcp):
             renewed = output.count("Cert success")
             skipped = output.count("Skip")
 
+            # Reload any renewed certs into HAProxy
             if renewed > 0:
-                return f"Renewed {renewed} certificate(s), skipped {skipped}"
+                domains = load_cert_config()
+                reloaded = 0
+                for domain in domains:
+                    success, _ = load_cert_to_haproxy(domain)
+                    if success:
+                        reloaded += 1
+                return f"Renewed {renewed} certificate(s), reloaded {reloaded} into HAProxy"
             elif skipped > 0:
                 return f"No certificates due for renewal ({skipped} checked)"
             elif result.returncode != 0:
@@ -286,14 +469,21 @@ def register_certificate_tools(mcp):
             return "Error: Invalid domain format"
 
         cert_dir = os.path.join(ACME_HOME, f"{domain}_ecc")
-        pem_path = os.path.join(CERTS_DIR, f"{domain}.pem")
+        host_path, _ = get_pem_paths(domain)
 
-        if not os.path.exists(cert_dir) and not os.path.exists(pem_path):
+        if not os.path.exists(cert_dir) and not os.path.exists(host_path):
             return f"Error: No certificate found for {domain}"
 
         errors = []
         deleted = []
 
+        # Unload from HAProxy first (zero-downtime)
+        success, msg = unload_cert_from_haproxy(domain)
+        if success:
+            deleted.append(f"HAProxy ({msg})")
+        else:
+            errors.append(f"HAProxy unload: {msg}")
+
         # Remove from acme.sh
         if os.path.exists(cert_dir):
             try:
@@ -305,28 +495,49 @@ def register_certificate_tools(mcp):
                 if result.returncode == 0:
                     deleted.append("acme.sh")
                 else:
-                    errors.append(f"acme.sh removal: {result.stderr}")
+                    errors.append(f"acme.sh: {result.stderr}")
             except Exception as e:
-                errors.append(f"acme.sh removal: {e}")
+                errors.append(f"acme.sh: {e}")
 
         # Remove PEM file
-        if os.path.exists(pem_path):
+        if os.path.exists(host_path):
             try:
-                os.remove(pem_path)
-                deleted.append("HAProxy PEM")
-
-                # Signal HAProxy to reload certs
-                subprocess.run(
-                    ["podman", "exec", HAPROXY_CONTAINER, "kill", "-USR2", "1"],
-                    capture_output=True, timeout=SUBPROCESS_TIMEOUT
-                )
+                os.remove(host_path)
+                deleted.append("PEM file")
             except Exception as e:
-                errors.append(f"PEM removal: {e}")
+                errors.append(f"PEM file: {e}")
+
+        # Remove from config
+        remove_cert_from_config(domain)
 
         result_parts = []
         if deleted:
-            result_parts.append(f"Deleted from: {', '.join(deleted)}")
+            result_parts.append(f"Deleted: {', '.join(deleted)}")
         if errors:
             result_parts.append(f"Errors: {'; '.join(errors)}")
 
         return "\n".join(result_parts) if result_parts else f"Certificate {domain} deleted"
+
+    @mcp.tool()
+    def haproxy_load_cert(
+        domain: Annotated[str, Field(description="Domain name to load certificate for")]
+    ) -> str:
+        """Load/reload a certificate into HAProxy (zero-downtime).
+
+        Use after manually updating a certificate file.
+
+        Example: haproxy_load_cert("example.com")
+        """
+        if not validate_domain(domain):
+            return "Error: Invalid domain format"
+
+        host_path, _ = get_pem_paths(domain)
+        if not os.path.exists(host_path):
+            return f"Error: PEM file not found: {host_path}"
+
+        success, msg = load_cert_to_haproxy(domain)
+        if success:
+            add_cert_to_config(domain)
+            return f"Certificate {domain} loaded into HAProxy ({msg})"
+        else:
+            return f"Error loading certificate: {msg}"
diff --git a/haproxy_mcp/tools/configuration.py b/haproxy_mcp/tools/configuration.py
index 8b0b6b3..a03fae1 100644
--- a/haproxy_mcp/tools/configuration.py
+++ b/haproxy_mcp/tools/configuration.py
@@ -95,7 +95,7 @@ def restore_servers_from_config() -> int:
 
 
 def startup_restore() -> None:
-    """Restore servers from config file on startup."""
+    """Restore servers and certificates from config files on startup."""
     # Wait for HAProxy to be ready
     for _ in range(STARTUP_RETRY_COUNT):
         try:
@@ -107,6 +107,7 @@ def startup_restore() -> None:
         logger.warning("HAProxy not ready, skipping restore")
         return
 
+    # Restore servers
     try:
         count = restore_servers_from_config()
         if count > 0:
@@ -114,6 +115,15 @@ def startup_restore() -> None:
     except (HaproxyError, OSError, ValueError) as e:
         logger.warning("Failed to restore servers: %s", e)
 
+    # Restore certificates
+    try:
+        from .certificates import restore_certificates
+        cert_count = restore_certificates()
+        if cert_count > 0:
+            logger.info("Restored %d certificates from config", cert_count)
+    except Exception as e:
+        logger.warning("Failed to restore certificates: %s", e)
+
 
 def register_config_tools(mcp):
     """Register configuration management tools with MCP server."""