diff --git a/internal/domain/config/wrangler.go b/internal/domain/config/wrangler.go
index 783853f..d7fe5ea 100644
--- a/internal/domain/config/wrangler.go
+++ b/internal/domain/config/wrangler.go
@@ -1,5 +1,10 @@
 package config
 
+import (
+	"encoding/json"
+	"reflect"
+)
+
 type WranglerConfig struct {
 	Name              string                       `json:"name"`
 	Main              string                       `json:"main"`
@@ -12,6 +17,7 @@ type WranglerConfig struct {
 	R2Buckets         []WranglerR2Bucket           `json:"r2_buckets,omitempty"`
 	Routes            []WranglerRoute              `json:"routes,omitempty"`
 	Env               map[string]WranglerEnvConfig `json:"env,omitempty"`
+	Extra             map[string]json.RawMessage   `json:"-"`
 }
 
 type WranglerObservability struct {
@@ -19,13 +25,14 @@ type WranglerObservability struct {
 }
 
 type WranglerEnvConfig struct {
-	Name         string                `json:"name,omitempty"`
-	AI           *WranglerAIBinding    `json:"ai,omitempty"`
-	Vars         map[string]string     `json:"vars,omitempty"`
-	KVNamespaces []WranglerKVNamespace `json:"kv_namespaces,omitempty"`
-	D1Databases  []WranglerD1Database  `json:"d1_databases,omitempty"`
-	R2Buckets    []WranglerR2Bucket    `json:"r2_buckets,omitempty"`
-	Routes       []WranglerRoute       `json:"routes,omitempty"`
+	Name         string                     `json:"name,omitempty"`
+	AI           *WranglerAIBinding         `json:"ai,omitempty"`
+	Vars         map[string]string          `json:"vars,omitempty"`
+	KVNamespaces []WranglerKVNamespace      `json:"kv_namespaces,omitempty"`
+	D1Databases  []WranglerD1Database       `json:"d1_databases,omitempty"`
+	R2Buckets    []WranglerR2Bucket         `json:"r2_buckets,omitempty"`
+	Routes       []WranglerRoute            `json:"routes,omitempty"`
+	Extra        map[string]json.RawMessage `json:"-"`
 }
 
 type WranglerAIBinding struct {
@@ -57,3 +64,168 @@ type WranglerRoute struct {
 	ZoneID       string `json:"zone_id,omitempty"`
 	CustomDomain bool   `json:"custom_domain,omitempty"`
 }
+
+func (w *WranglerConfig) UnmarshalJSON(data []byte) error {
+	type alias WranglerConfig
+	var decoded alias
+	if err := json.Unmarshal(data, &decoded); err != nil {
+		return err
+	}
+
+	var raw map[string]json.RawMessage
+	if err := json.Unmarshal(data, &raw); err != nil {
+		return err
+	}
+	deleteKnownWranglerKeys(raw)
+
+	*w = WranglerConfig(decoded)
+	if len(raw) > 0 {
+		w.Extra = raw
+	} else {
+		w.Extra = nil
+	}
+	return nil
+}
+
+func (w WranglerConfig) MarshalJSON() ([]byte, error) {
+	raw := cloneRawMap(w.Extra)
+	deleteKnownWranglerKeys(raw)
+
+	putString(raw, "name", w.Name)
+	putString(raw, "main", w.Main)
+	putValue(raw, "compatibility_date", w.CompatibilityDate)
+	putValue(raw, "observability", w.Observability)
+	putValue(raw, "ai", w.AI)
+	putValue(raw, "vars", w.Vars)
+	putValue(raw, "kv_namespaces", w.KVNamespaces)
+	putValue(raw, "d1_databases", w.D1Databases)
+	putValue(raw, "r2_buckets", w.R2Buckets)
+	putValue(raw, "routes", w.Routes)
+	putValue(raw, "env", w.Env)
+
+	return json.Marshal(raw)
+}
+
+func (w *WranglerEnvConfig) UnmarshalJSON(data []byte) error {
+	type alias WranglerEnvConfig
+	var decoded alias
+	if err := json.Unmarshal(data, &decoded); err != nil {
+		return err
+	}
+
+	var raw map[string]json.RawMessage
+	if err := json.Unmarshal(data, &raw); err != nil {
+		return err
+	}
+	deleteKnownWranglerEnvKeys(raw)
+
+	*w = WranglerEnvConfig(decoded)
+	if len(raw) > 0 {
+		w.Extra = raw
+	} else {
+		w.Extra = nil
+	}
+	return nil
+}
+
+func (w WranglerEnvConfig) MarshalJSON() ([]byte, error) {
+	raw := cloneRawMap(w.Extra)
+	deleteKnownWranglerEnvKeys(raw)
+
+	putString(raw, "name", w.Name)
+	putValue(raw, "ai", w.AI)
+	putValue(raw, "vars", w.Vars)
+	putValue(raw, "kv_namespaces", w.KVNamespaces)
+	putValue(raw, "d1_databases", w.D1Databases)
+	putValue(raw, "r2_buckets", w.R2Buckets)
+	putValue(raw, "routes", w.Routes)
+
+	return json.Marshal(raw)
+}
+
+func cloneRawMap(source map[string]json.RawMessage) map[string]json.RawMessage {
+	if len(source) == 0 {
+		return map[string]json.RawMessage{}
+	}
+	cloned := make(map[string]json.RawMessage, len(source))
+	for key, value := range source {
+		cloned[key] = append(json.RawMessage(nil), value...)
+	}
+	return cloned
+}
+
+func deleteKnownWranglerKeys(raw map[string]json.RawMessage) {
+	delete(raw, "name")
+	delete(raw, "main")
+	delete(raw, "compatibility_date")
+	delete(raw, "observability")
+	delete(raw, "ai")
+	delete(raw, "vars")
+	delete(raw, "kv_namespaces")
+	delete(raw, "d1_databases")
+	delete(raw, "r2_buckets")
+	delete(raw, "routes")
+	delete(raw, "env")
+}
+
+func deleteKnownWranglerEnvKeys(raw map[string]json.RawMessage) {
+	delete(raw, "name")
+	delete(raw, "ai")
+	delete(raw, "vars")
+	delete(raw, "kv_namespaces")
+	delete(raw, "d1_databases")
+	delete(raw, "r2_buckets")
+	delete(raw, "routes")
+}
+
+func putString(raw map[string]json.RawMessage, key, value string) {
+	if value == "" {
+		delete(raw, key)
+		return
+	}
+	putValue(raw, key, value)
+}
+
+func putValue(raw map[string]json.RawMessage, key string, value any) {
+	if isEmptyJSONValue(value) {
+		delete(raw, key)
+		return
+	}
+	data, err := json.Marshal(value)
+	if err != nil {
+		return
+	}
+	raw[key] = data
+}
+
+func isEmptyJSONValue(value any) bool {
+	if value == nil {
+		return true
+	}
+	rv := reflect.ValueOf(value)
+	switch rv.Kind() {
+	case reflect.Pointer, reflect.Interface, reflect.Map, reflect.Slice:
+		if rv.IsNil() {
+			return true
+		}
+	}
+
+	switch typed := value.(type) {
+	case string:
+		return typed == ""
+	case map[string]string:
+		return len(typed) == 0
+	case map[string]WranglerEnvConfig:
+		return len(typed) == 0
+	case []WranglerKVNamespace:
+		return len(typed) == 0
+	case []WranglerD1Database:
+		return len(typed) == 0
+	case []WranglerR2Bucket:
+		return len(typed) == 0
+	case []WranglerRoute:
+		return len(typed) == 0
+	default:
+		return false
+	}
+}
diff --git a/internal/domain/config/wrangler_test.go b/internal/domain/config/wrangler_test.go
new file mode 100644
index 0000000..8d37fa7
--- /dev/null
+++ b/internal/domain/config/wrangler_test.go
@@ -0,0 +1,76 @@
+package config
+
+import (
+	"encoding/json"
+	"strings"
+	"testing"
+)
+
+func TestWranglerConfigRoundTripPreservesUnknownFields(t *testing.T) {
+	input := []byte(`{
+  "name": "demo-worker",
+  "main": "dist/worker.mjs",
+  "compatibility_date": "2026-03-19",
+  "ai": { "binding": "AI", "remote": true },
+  "unsafe": { "bindings": [{ "name": "EXTRA" }] },
+  "env": {
+    "production": {
+      "vars": { "FOO": "bar" },
+      "durable_objects": {
+        "bindings": [{ "name": "COUNTER", "class_name": "Counter" }]
+      }
+    }
+  }
+}`)
+
+	var cfg WranglerConfig
+	if err := json.Unmarshal(input, &cfg); err != nil {
+		t.Fatalf("unmarshal wrangler config: %v", err)
+	}
+
+	cfg.Vars = map[string]string{"BAR": "baz"}
+
+	output, err := json.Marshal(cfg)
+	if err != nil {
+		t.Fatalf("marshal wrangler config: %v", err)
+	}
+
+	text := string(output)
+	if !strings.Contains(text, `"unsafe":{"bindings":[{"name":"EXTRA"}]}`) {
+		t.Fatalf("unknown top-level field was not preserved: %s", text)
+	}
+	if !strings.Contains(text, `"durable_objects":{"bindings":[{"name":"COUNTER","class_name":"Counter"}]}`) {
+		t.Fatalf("unknown env field was not preserved: %s", text)
+	}
+	if !strings.Contains(text, `"vars":{"BAR":"baz"}`) {
+		t.Fatalf("known var update was not written: %s", text)
+	}
+}
+
+func TestWranglerConfigMarshalDoesNotResurrectClearedKnownFields(t *testing.T) {
+	input := []byte(`{
+  "name": "demo-worker",
+  "ai": { "binding": "AI", "remote": true },
+  "unsafe": { "bindings": [{ "name": "EXTRA" }] }
+}`)
+
+	var cfg WranglerConfig
+	if err := json.Unmarshal(input, &cfg); err != nil {
+		t.Fatalf("unmarshal wrangler config: %v", err)
+	}
+
+	cfg.AI = nil
+
+	output, err := json.Marshal(cfg)
+	if err != nil {
+		t.Fatalf("marshal wrangler config: %v", err)
+	}
+
+	text := string(output)
+	if strings.Contains(text, `"ai":`) {
+		t.Fatalf("cleared known field should not be preserved from extras: %s", text)
+	}
+	if !strings.Contains(text, `"unsafe":{"bindings":[{"name":"EXTRA"}]}`) {
+		t.Fatalf("unknown field should still be preserved: %s", text)
+	}
+}