diff --git a/go/daemon/config.go b/go/daemon/config.go
index b717eb1..8423ffb 100644
--- a/go/daemon/config.go
+++ b/go/daemon/config.go
@@ -8,14 +8,34 @@ import (
 	"isle/daemon/network"
 )
 
+// getDeprecatedNetworkConfig will return the NetworkConfig configured in the
+// deprecated configuration format, or nil if the deprecated format is not used.
+//
+// In the deprecated format it is not possible to explicitly know which network
+// a NetworkConfig is intended for, so the Daemon can only allow a single
+// network to be joined when using this format.
+//
+// DEPRECATED
+func getDeprecatedNetworkConfig(
+	networkConfigs map[string]daecommon.NetworkConfig,
+) *daecommon.NetworkConfig {
+	if len(networkConfigs) != 1 {
+		return nil
+	}
+
+	if c, ok := networkConfigs[daecommon.DeprecatedNetworkID]; ok {
+		return &c
+	}
+
+	return nil
+}
+
 func pickNetworkConfig(
 	networkConfigs map[string]daecommon.NetworkConfig,
 	creationParams bootstrap.CreationParams,
 ) *daecommon.NetworkConfig {
-	if len(networkConfigs) == 1 { // DEPRECATED
-		if c, ok := networkConfigs[daecommon.DeprecatedNetworkID]; ok {
-			return &c
-		}
+	if c := getDeprecatedNetworkConfig(networkConfigs); c != nil {
+		return c
 	}
 
 	for searchStr, networkConfig := range networkConfigs {
diff --git a/go/daemon/daemon.go b/go/daemon/daemon.go
index 74ad137..5d1e2f8 100644
--- a/go/daemon/daemon.go
+++ b/go/daemon/daemon.go
@@ -71,6 +71,11 @@ func New(
 		return nil, fmt.Errorf("listing loadable networks: %w", err)
 	}
 
+	if getDeprecatedNetworkConfig(daemonConfig.Networks) != nil &&
+		len(loadableNetworks) > 1 {
+		return nil, errors.New("Deprecated config format cannot be used when there are more than one loadable networks")
+	}
+
 	if err := validateConfig(
 		ctx, networkLoader, daemonConfig, loadableNetworks,
 	); err != nil {
@@ -131,6 +136,13 @@ func (d *Daemon) CreateNetwork(
 	d.l.Lock()
 	defer d.l.Unlock()
 
+	if getDeprecatedNetworkConfig(d.daemonConfig.Networks) != nil &&
+		len(d.networks) > 0 {
+		return network.ErrInvalidConfig.WithData(
+			"Cannot use deprecated configuration file format while joined to more than one network",
+		)
+	}
+
 	var (
 		networkConfig = pickNetworkConfig(
 			d.daemonConfig.Networks, creationParams,
@@ -182,6 +194,13 @@ func (d *Daemon) JoinNetwork(
 	d.l.Lock()
 	defer d.l.Unlock()
 
+	if getDeprecatedNetworkConfig(d.daemonConfig.Networks) != nil &&
+		len(d.networks) > 0 {
+		return network.ErrInvalidConfig.WithData(
+			"Cannot use deprecated configuration file format while joined to more than one network",
+		)
+	}
+
 	var (
 		creationParams = newBootstrap.Bootstrap.NetworkCreationParams
 		networkID      = creationParams.ID