diff --git a/internal/mode/static/nginx/config/servers.go b/internal/mode/static/nginx/config/servers.go
index 0e2c58f10a..f7d76e2e80 100644
--- a/internal/mode/static/nginx/config/servers.go
+++ b/internal/mode/static/nginx/config/servers.go
@@ -4,6 +4,7 @@ import (
 	"encoding/json"
 	"fmt"
 	"maps"
+	"slices"
 	"strconv"
 	"strings"
 	gotemplate "text/template"
@@ -812,7 +813,15 @@ func generateProxySetHeaders(
 		})
 	}
 
-	return append(proxySetHeaders, baseHeaders...)
+	for _, header := range baseHeaders {
+		if !slices.ContainsFunc(proxySetHeaders, func(h http.Header) bool {
+			return header.Name == h.Name
+		}) {
+			proxySetHeaders = append(proxySetHeaders, header)
+		}
+	}
+
+	return proxySetHeaders
 }
 
 func generateResponseHeaders(filters *dataplane.HTTPFilters) http.ResponseHeaders {
diff --git a/internal/mode/static/nginx/config/servers_test.go b/internal/mode/static/nginx/config/servers_test.go
index 29d84d0c77..56da44f1fa 100644
--- a/internal/mode/static/nginx/config/servers_test.go
+++ b/internal/mode/static/nginx/config/servers_test.go
@@ -3146,6 +3146,54 @@ func TestGenerateProxySetHeaders(t *testing.T) {
 			}, httpBaseHeaders...),
 			baseHeaders: httpBaseHeaders,
 		},
+		{
+			msg: "header filter overwrite base header",
+			filters: &dataplane.HTTPFilters{
+				RequestHeaderModifiers: &dataplane.HTTPHeaderFilter{
+					Set: []dataplane.HTTPHeader{
+						{
+							Name:  "X-Forwarded-Proto",
+							Value: "new-proto",
+						},
+					},
+				},
+			},
+			expectedHeaders: []http.Header{
+				{
+					Name:  "X-Forwarded-Proto",
+					Value: "new-proto",
+				},
+				{
+					Name:  "Host",
+					Value: "$gw_api_compliant_host",
+				},
+				{
+					Name:  "X-Forwarded-For",
+					Value: "$proxy_add_x_forwarded_for",
+				},
+				{
+					Name:  "X-Real-IP",
+					Value: "$remote_addr",
+				},
+				{
+					Name:  "X-Forwarded-Host",
+					Value: "$host",
+				},
+				{
+					Name:  "X-Forwarded-Port",
+					Value: "$server_port",
+				},
+				{
+					Name:  "Upgrade",
+					Value: "$http_upgrade",
+				},
+				{
+					Name:  "Connection",
+					Value: "$connection_upgrade",
+				},
+			},
+			baseHeaders: httpBaseHeaders,
+		},
 		{
 			msg: "with url rewrite hostname",
 			filters: &dataplane.HTTPFilters{