diff --git a/internal/watcher/instance/nginx_config_parser.go b/internal/watcher/instance/nginx_config_parser.go
index 26e698ed6..605e287c5 100644
--- a/internal/watcher/instance/nginx_config_parser.go
+++ b/internal/watcher/instance/nginx_config_parser.go
@@ -139,7 +139,10 @@ func (ncp *NginxConfigParser) createNginxConfigContext(
 					nginxConfigContext.Files = append(nginxConfigContext.Files, rootFiles...)
 				case "ssl_certificate", "proxy_ssl_certificate", "ssl_client_certificate", "ssl_trusted_certificate":
 					sslCertFile := ncp.sslCert(ctx, directive.Args[0], rootDir)
-					nginxConfigContext.Files = append(nginxConfigContext.Files, sslCertFile)
+					if !ncp.isDuplicateFile(nginxConfigContext.Files, sslCertFile) {
+						nginxConfigContext.Files = append(nginxConfigContext.Files, sslCertFile)
+					}
+
 				case "app_protect_security_log":
 					if len(directive.Args) > 1 {
 						syslogArg := directive.Args[1]
@@ -349,6 +352,16 @@ func (ncp *NginxConfigParser) sslCert(ctx context.Context, file, rootDir string)
 	return sslCertFile
 }
 
+func (ncp *NginxConfigParser) isDuplicateFile(nginxConfigContextFiles []*mpi.File, newFile *mpi.File) bool {
+	for _, nginxConfigContextFile := range nginxConfigContextFiles {
+		if nginxConfigContextFile.GetFileMeta().GetName() == newFile.GetFileMeta().GetName() {
+			return true
+		}
+	}
+
+	return false
+}
+
 func (ncp *NginxConfigParser) crossplaneConfigTraverse(
 	ctx context.Context,
 	root *crossplane.Config,
diff --git a/internal/watcher/instance/nginx_config_parser_test.go b/internal/watcher/instance/nginx_config_parser_test.go
index c0c320831..4c9174aaf 100644
--- a/internal/watcher/instance/nginx_config_parser_test.go
+++ b/internal/watcher/instance/nginx_config_parser_test.go
@@ -14,6 +14,8 @@ import (
 	"os"
 	"testing"
 
+	"google.golang.org/protobuf/types/known/timestamppb"
+
 	"github.com/google/go-cmp/cmp"
 	"github.com/nginx/agent/v3/internal/model"
 	"github.com/nginx/agent/v3/pkg/files"
@@ -960,3 +962,91 @@ func TestNginxConfigParser_ignoreLog(t *testing.T) {
 		})
 	}
 }
+
+func TestNginxConfigParser_checkDuplicate(t *testing.T) {
+	fileContent := []byte("location /test {\n    return 200 \"Test location\\n\";\n}")
+	fileContentNew := []byte("some test data")
+	fileHash := files.GenerateHash(fileContent)
+	fileHashNew := files.GenerateHash(fileContentNew)
+
+	tests := []struct {
+		file     *mpi.File
+		name     string
+		expected bool
+	}{
+		{
+			name: "Test 1: File already in files",
+			file: &mpi.File{
+				FileMeta: &mpi.FileMeta{
+					Name:         "/etc/nginx/certs/nginx-repo.crt",
+					Hash:         fileHashNew,
+					ModifiedTime: timestamppb.Now(),
+					Permissions:  "0640",
+					Size:         0,
+				},
+			},
+			expected: true,
+		},
+		{
+			name: "Test 2: File not in files",
+			file: &mpi.File{
+				FileMeta: &mpi.FileMeta{
+					Name:         "/etc/nginx/certs/nginx-repo-new.crt",
+					Hash:         fileHashNew,
+					ModifiedTime: timestamppb.Now(),
+					Permissions:  "0640",
+					Size:         0,
+				},
+			},
+			expected: false,
+		},
+	}
+
+	nginxConfigContextFiles := model.NginxConfigContext{
+		Files: []*mpi.File{
+			{
+				FileMeta: &mpi.FileMeta{
+					Name:         "/etc/nginx/certs/nginx-repo.crt",
+					Hash:         fileHash,
+					ModifiedTime: timestamppb.Now(),
+					Permissions:  "0640",
+					Size:         0,
+				},
+			},
+			{
+				FileMeta: &mpi.FileMeta{
+					Name:         "/etc/nginx/keys/nginx-repo.key",
+					Hash:         fileHash,
+					ModifiedTime: timestamppb.Now(),
+					Permissions:  "0640",
+					Size:         0,
+				},
+			},
+			{
+				FileMeta: &mpi.FileMeta{
+					Name:         "/etc/nginx/keys/inline_key.pem",
+					Hash:         fileHash,
+					ModifiedTime: timestamppb.Now(),
+					Permissions:  "0640",
+					Size:         0,
+				},
+			},
+			{
+				FileMeta: &mpi.FileMeta{
+					Name:         "/etc/nginx/certs/inline_cert.pem",
+					Hash:         fileHash,
+					ModifiedTime: timestamppb.Now(),
+					Permissions:  "0640",
+					Size:         0,
+				},
+			},
+		},
+	}
+
+	for _, test := range tests {
+		ncp := NewNginxConfigParser(types.AgentConfig())
+		t.Run(test.name, func(t *testing.T) {
+			assert.Equal(t, test.expected, ncp.isDuplicateFile(nginxConfigContextFiles.Files, test.file))
+		})
+	}
+}