diff --git a/cmd/serve.go b/cmd/serve.go
index 66c29713..d784f91c 100644
--- a/cmd/serve.go
+++ b/cmd/serve.go
@@ -7,6 +7,7 @@ import (
 	netHTTP "net/http"
 	"os"
 	"runtime"
+	"strconv"
 	"strings"
 
 	"github.com/mitchellh/mapstructure"
@@ -117,12 +118,20 @@ and exports them to Kafka.`,
 				continue
 			}
 			// From AKVORADO_SQUID_PURPLE_QUIRK=47, we
-			// build a map "squid -> purple -> quirk -> 47"
+			// build a map "squid -> purple -> quirk ->
+			// 47". From AKVORADO_SQUID_3_PURPLE=47, we
+			// build "squid[3] -> purple -> 47"
 			var rawConfig interface{}
 			rawConfig = kv[1]
 			for i := len(kk) - 1; i > 0; i-- {
-				rawConfig = map[string]interface{}{
-					kk[i]: rawConfig,
+				if index, err := strconv.Atoi(kk[i]); err == nil {
+					newRawConfig := make([]interface{}, index+1)
+					newRawConfig[index] = rawConfig
+					rawConfig = newRawConfig
+				} else {
+					rawConfig = map[string]interface{}{
+						kk[i]: rawConfig,
+					}
 				}
 			}
 			if err := decoder.Decode(rawConfig); err != nil {
diff --git a/cmd/serve_test.go b/cmd/serve_test.go
index 40a48c2e..12bffc4a 100644
--- a/cmd/serve_test.go
+++ b/cmd/serve_test.go
@@ -106,10 +106,15 @@ core:
 	ioutil.WriteFile(configFile, []byte(config), 0644)
 
 	// Environment
-	os.Setenv("AKVORADO_FLOW_WORKERS", "3")
 	os.Setenv("AKVORADO_SNMP_CACHEDURATION", "22m")
 	os.Setenv("AKVORADO_SNMP_DEFAULTCOMMUNITY", "privateer")
 	os.Setenv("AKVORADO_KAFKA_BROKERS", "127.0.0.1:9092,127.0.0.2:9092")
+	os.Setenv("AKVORADO_FLOW_WORKERS", "3")
+	os.Setenv("AKVORADO_FLOW_INPUTS_0_LISTEN", "0.0.0.0:2056")
+	// We may be lucky or the environment is keeping order
+	os.Setenv("AKVORADO_FLOW_INPUTS_1_TYPE", "file")
+	os.Setenv("AKVORADO_FLOW_INPUTS_1_DECODER", "netflow")
+	os.Setenv("AKVORADO_FLOW_INPUTS_1_PATHS", "f1,f2")
 
 	// Start serves with it
 	root := cmd.RootCmd
@@ -127,8 +132,23 @@ core:
 	if err := yaml.Unmarshal(buf.Bytes(), &got); err != nil {
 		t.Fatalf("Unmarshal() error:\n%+v", err)
 	}
-	want(t, got["flow"]["workers"], 3)
 	want(t, got["snmp"]["cacheduration"], "22m0s")
 	want(t, got["snmp"]["defaultcommunity"], "privateer")
 	want(t, got["kafka"]["brokers"], []string{"127.0.0.1:9092", "127.0.0.2:9092"})
+	want(t, got["flow"], map[string]interface{}{
+		"inputs": []map[string]interface{}{
+			{
+				"type":      "udp",
+				"decoder":   "netflow",
+				"listen":    "0.0.0.0:2056",
+				"queuesize": 100000,
+				"workers":   5,
+			}, {
+				"type":    "file",
+				"decoder": "netflow",
+				"paths":   []string{"f1", "f2"},
+			},
+		},
+		"workers": 3,
+	})
 }
diff --git a/flow/config.go b/flow/config.go
index f38045a5..c59549f7 100644
--- a/flow/config.go
+++ b/flow/config.go
@@ -112,6 +112,10 @@ func ConfigurationUnmarshalerHook() mapstructure.DecodeHookFunc {
 
 		// Alter config with a copy of the concrete type
 		original := reflect.Indirect(reflect.ValueOf(input))
+		if !configField.IsNil() && configField.Elem().Type().Elem() == reflect.TypeOf(input).Elem() {
+			// Use the value we already have instead of default.
+			original = reflect.Indirect(configField.Elem())
+		}
 		copy := reflect.New(original.Type())
 		copy.Elem().Set(reflect.ValueOf(original.Interface()))
 		configField.Set(copy)
diff --git a/flow/config_test.go b/flow/config_test.go
index e0d19d85..dadf37fb 100644
--- a/flow/config_test.go
+++ b/flow/config_test.go
@@ -107,7 +107,11 @@ func TestDecodeConfiguration(t *testing.T) {
 				Workers: 10,
 				Inputs: []InputConfiguration{{
 					Decoder: "netflow",
-					Config:  &udp.DefaultConfiguration,
+					Config: &udp.Configuration{
+						Workers:   2,
+						QueueSize: 100,
+						Listen:    "127.0.0.1:2055",
+					},
 				}},
 			},
 			Source: map[string]interface{}{
@@ -122,8 +126,8 @@ func TestDecodeConfiguration(t *testing.T) {
 				Inputs: []InputConfiguration{{
 					Decoder: "netflow",
 					Config: &udp.Configuration{
-						Workers:   1,
-						QueueSize: 100000,
+						Workers:   2,
+						QueueSize: 100,
 						Listen:    "192.0.2.1:2055",
 					},
 				}},
@@ -160,7 +164,7 @@ func TestDecodeConfiguration(t *testing.T) {
 		})
 	}
 
-	// Check we didn't alter the default value
+	// Check we didn't alter the default value for UDP
 	if diff := helpers.Diff(udp.DefaultConfiguration, udp.Configuration{
 		Workers:   1,
 		QueueSize: 100000,