diff --git a/command/agent/config.go b/command/agent/config.go
index 1f7793146..2a78dcd36 100644
--- a/command/agent/config.go
+++ b/command/agent/config.go
@@ -264,9 +264,6 @@ type Telemetry struct {
 
 // Autopilot is used to configure helpful features for operating Consul servers.
 type Autopilot struct {
-	// RaftProtocolVersion sets the Raft protocol version to use on this server.
-	RaftProtocolVersion int `mapstructure:"raft_protocol"`
-
 	// DeadServerCleanup enables the automatic cleanup of dead servers when new ones
 	// are added to the peer list. Defaults to true.
 	DeadServerCleanup *bool `mapstructure:"dead_server_cleanup"`
@@ -405,6 +402,9 @@ type Config struct {
 	// Protocol is the Consul protocol version to use.
 	Protocol int `mapstructure:"protocol"`
 
+	// RaftProtocol sets the Raft protocol version to use on this server.
+	RaftProtocol int `mapstructure:"raft_protocol"`
+
 	// EnableDebug is used to enable various debugging features
 	EnableDebug bool `mapstructure:"enable_debug"`
 
@@ -1299,6 +1299,9 @@ func MergeConfig(a, b *Config) *Config {
 	if b.Protocol > 0 {
 		result.Protocol = b.Protocol
 	}
+	if b.RaftProtocol != 0 {
+		result.RaftProtocol = b.RaftProtocol
+	}
 	if b.NodeID != "" {
 		result.NodeID = b.NodeID
 	}
@@ -1347,9 +1350,6 @@ func MergeConfig(a, b *Config) *Config {
 	if b.SkipLeaveOnInt != nil {
 		result.SkipLeaveOnInt = b.SkipLeaveOnInt
 	}
-	if b.Autopilot.RaftProtocolVersion != 0 {
-		result.Autopilot.RaftProtocolVersion = b.Autopilot.RaftProtocolVersion
-	}
 	if b.Autopilot.DeadServerCleanup != nil {
 		result.Autopilot.DeadServerCleanup = b.Autopilot.DeadServerCleanup
 	}
diff --git a/command/agent/config_test.go b/command/agent/config_test.go
index 1510c3fdd..cbd00216a 100644
--- a/command/agent/config_test.go
+++ b/command/agent/config_test.go
@@ -285,6 +285,17 @@ func TestDecodeConfig(t *testing.T) {
 		t.Fatalf("bad: %#v", config)
 	}
 
+	// raft protocol
+	input = `{"raft_protocol": 3}`
+	config, err = DecodeConfig(bytes.NewReader([]byte(input)))
+	if err != nil {
+		t.Fatalf("err: %s", err)
+	}
+
+	if config.RaftProtocol != 3 {
+		t.Fatalf("bad: %#v", config)
+	}
+
 	// Node metadata fields
 	input = `{"node_meta": {"thing1": "1", "thing2": "2"}}`
 	config, err = DecodeConfig(bytes.NewReader([]byte(input)))
@@ -1099,14 +1110,11 @@ func TestDecodeConfig_Performance(t *testing.T) {
 }
 
 func TestDecodeConfig_Autopilot(t *testing.T) {
-	input := `{"autopilot": { "raft_protocol": 3, "dead_server_cleanup": true }}`
+	input := `{"autopilot": { "dead_server_cleanup": true }}`
 	config, err := DecodeConfig(bytes.NewReader([]byte(input)))
 	if err != nil {
 		t.Fatalf("err: %s", err)
 	}
-	if config.Autopilot.RaftProtocolVersion != 3 {
-		t.Fatalf("bad: raft_protocol isn't set: %#v", config)
-	}
 	if config.Autopilot.DeadServerCleanup == nil || !*config.Autopilot.DeadServerCleanup {
 		t.Fatalf("bad: dead_server_cleanup isn't set: %#v", config)
 	}
@@ -1633,8 +1641,8 @@ func TestMergeConfig(t *testing.T) {
 		Server:                 true,
 		LeaveOnTerm:            Bool(true),
 		SkipLeaveOnInt:         Bool(true),
+		RaftProtocol:           3,
 		Autopilot:              Autopilot{
-			RaftProtocolVersion: 3,
 			DeadServerCleanup:   Bool(true),
 		},
 		EnableDebug:            true,
diff --git a/consul/config.go b/consul/config.go
index 01d80711e..7cfc09470 100644
--- a/consul/config.go
+++ b/consul/config.go
@@ -366,8 +366,9 @@ func DefaultConfig() *Config {
 	conf.SerfLANConfig.MemberlistConfig.BindPort = DefaultLANSerfPort
 	conf.SerfWANConfig.MemberlistConfig.BindPort = DefaultWANSerfPort
 
-	// Enable interoperability with unversioned Raft library, and don't
-	// start using new ID-based features yet.
+	// TODO: default to 3 in Consul 0.9
+	// Use a transitional version of the raft protocol to interoperate with
+	// versions 1 and 3
 	conf.RaftConfig.ProtocolVersion = 2
 	conf.ScaleRaft(DefaultRaftMultiplier)
 
diff --git a/consul/leader.go b/consul/leader.go
index 8197a5e0f..93fad4361 100644
--- a/consul/leader.go
+++ b/consul/leader.go
@@ -620,16 +620,17 @@ func (s *Server) removeConsulServer(m serf.Member, port int) error {
 	for _, server := range configFuture.Configuration().Servers {
 		// If we understand the new add/remove APIs and the server was added by ID, use the new remove API
 		if minRaftProtocol >= 2 && server.ID == raft.ServerID(parts.ID) {
-			s.logger.Printf("[INFO] consul: removing server via new api, %q %q", server.ID, server.Address)
+			s.logger.Printf("[INFO] consul: removing server by ID: %q", server.ID)
 			future := s.raft.RemoveServer(raft.ServerID(parts.ID), 0, 0)
 			if err := future.Error(); err != nil {
 				s.logger.Printf("[ERR] consul: failed to remove raft peer '%v': %v",
-					addr, err)
+					server.ID, err)
 				return err
 			}
 			break
 		} else if server.Address == raft.ServerAddress(addr) {
 			// If not, use the old remove API
+			s.logger.Printf("[INFO] consul: removing server by address: %q", server.Address)
 			future := s.raft.RemovePeer(raft.ServerAddress(addr))
 			if err := future.Error(); err != nil {
 				s.logger.Printf("[ERR] consul: failed to remove raft peer '%v': %v",
diff --git a/consul/util.go b/consul/util.go
index 0f5f33b21..f0d56e453 100644
--- a/consul/util.go
+++ b/consul/util.go
@@ -112,6 +112,11 @@ func ServerMinRaftProtocol(members []serf.Member) (int, error) {
 			minVersion = raftVsn
 		}
 	}
+
+	if minVersion == -1 {
+		return minVersion, fmt.Errorf("No servers found")
+	}
+
 	return minVersion, nil
 }