diff --git a/orderer/common/server/main.go b/orderer/common/server/main.go
index 7baf0c1c63a..ac2d0a8c499 100644
--- a/orderer/common/server/main.go
+++ b/orderer/common/server/main.go
@@ -384,31 +384,6 @@ func reuseListener(conf *localconfig.TopLevel) bool {
 	return false
 }
 
-// Extract system channel last config block
-func extractSysChanLastConfig(lf blockledger.Factory, bootstrapBlock *cb.Block) *cb.Block {
-	// Are we bootstrapping?
-	channelCount := len(lf.ChannelIDs())
-	if channelCount == 0 {
-		logger.Info("Bootstrapping because no existing channels")
-		return nil
-	}
-	logger.Infof("Not bootstrapping because of %d existing channels", channelCount)
-
-	systemChannelName, err := protoutil.GetChannelIDFromBlock(bootstrapBlock)
-	if err != nil {
-		logger.Panicf("Failed extracting system channel name from bootstrap block: %v", err)
-	}
-	systemChannelLedger, err := lf.GetOrCreate(systemChannelName)
-	if err != nil {
-		logger.Panicf("Failed getting system channel ledger: %v", err)
-	}
-	height := systemChannelLedger.Height()
-	lastConfigBlock := multichannel.ConfigBlockOrPanic(systemChannelLedger)
-	logger.Infof("System channel: name=%s, height=%d, last config block number=%d",
-		systemChannelName, height, lastConfigBlock.Header.Number)
-	return lastConfigBlock
-}
-
 // extractSystemChannel loops through all channels, and return the last
 // config block for the system channel. Returns nil if no system channel
 // was found.
@@ -418,6 +393,10 @@ func extractSystemChannel(lf blockledger.Factory, bccsp bccsp.BCCSP) *cb.Block {
 		if err != nil {
 			logger.Panicf("Failed getting channel %v's ledger: %v", cID, err)
 		}
+		if channelLedger.Height() == 0 {
+			continue // Some channels may have an empty ledger and (possibly) a join-block, skip those
+		}
+
 		channelConfigBlock := multichannel.ConfigBlockOrPanic(channelLedger)
 
 		err = onboarding.ValidateBootstrapBlock(channelConfigBlock, bccsp)
diff --git a/orderer/common/server/main_test.go b/orderer/common/server/main_test.go
index 7bdfb867247..a68c1c3bfff 100644
--- a/orderer/common/server/main_test.go
+++ b/orderer/common/server/main_test.go
@@ -394,7 +394,9 @@ func TestInitSystemChannelWithJoinBlock(t *testing.T) {
 
 }
 
-func TestExtractSysChanLastConfig(t *testing.T) {
+func TestExtractSystemChannel(t *testing.T) {
+	cryptoProvider, _ := sw.NewDefaultSecurityLevelWithKeystore(sw.NewDummyKeyStore())
+
 	tmpdir, err := ioutil.TempDir("", "main_test-")
 	require.NoError(t, err)
 	defer os.RemoveAll(tmpdir)
@@ -402,43 +404,52 @@ func TestExtractSysChanLastConfig(t *testing.T) {
 	rlf, err := fileledger.New(tmpdir, &disabled.Provider{})
 	require.NoError(t, err)
 
-	conf := genesisconfig.Load(genesisconfig.SampleInsecureSoloProfile, configtest.GetDevConfigDir())
-	genesisBlock := encoder.New(conf).GenesisBlock()
-
-	lastConf := extractSysChanLastConfig(rlf, genesisBlock)
-	require.Nil(t, lastConf)
+	lastConf := extractSystemChannel(rlf, cryptoProvider)
+	require.Nil(t, lastConf, "no ledgers")
 
-	rl, err := rlf.GetOrCreate("testchannelid")
+	_, err = rlf.GetOrCreate("emptychannelid")
 	require.NoError(t, err)
 
-	err = rl.Append(genesisBlock)
-	require.NoError(t, err)
+	lastConf = extractSystemChannel(rlf, cryptoProvider)
+	require.Nil(t, lastConf, "skip empty ledger")
 
-	lastConf = extractSysChanLastConfig(rlf, genesisBlock)
-	require.NotNil(t, lastConf)
-	require.Equal(t, uint64(0), lastConf.Header.Number)
+	conf := genesisconfig.Load(genesisconfig.SampleInsecureSoloProfile, configtest.GetDevConfigDir())
+	conf.Consortiums = nil
+	configBlock := encoder.New(conf).GenesisBlock()
+	rl, err := rlf.GetOrCreate("appchannelid")
+	err = rl.Append(configBlock)
+	require.NoError(t, err)
 
-	require.Panics(t, func() {
-		_ = extractSysChanLastConfig(rlf, nil)
-	})
+	lastConf = extractSystemChannel(rlf, cryptoProvider)
+	require.Nil(t, lastConf, "skip app ledger")
 
-	configTx, err := protoutil.CreateSignedEnvelope(common.HeaderType_CONFIG, "testchannelid", nil, &common.ConfigEnvelope{}, 0, 0)
+	conf = genesisconfig.Load(genesisconfig.SampleInsecureSoloProfile, configtest.GetDevConfigDir())
+	configBlock = encoder.New(conf).GenesisBlock()
+	rl, err = rlf.GetOrCreate("testchannelid")
+	err = rl.Append(configBlock)
 	require.NoError(t, err)
 
-	nextBlock := blockledger.CreateNextBlock(rl, []*common.Envelope{configTx})
-	nextBlock.Metadata.Metadata[common.BlockMetadataIndex_SIGNATURES] = protoutil.MarshalOrPanic(&common.Metadata{
+	lastConf = extractSystemChannel(rlf, cryptoProvider)
+	require.NotNil(t, lastConf, "get system channel genesis block")
+	require.Equal(t, uint64(0), lastConf.Header.Number)
+
+	// Make and append the next config block
+	prevHash := protoutil.BlockHeaderHash(configBlock.Header)
+	configBlock.Header.Number = 1
+	configBlock.Header.PreviousHash = prevHash
+	configBlock.Metadata.Metadata[common.BlockMetadataIndex_SIGNATURES] = protoutil.MarshalOrPanic(&common.Metadata{
 		Value: protoutil.MarshalOrPanic(&common.OrdererBlockMetadata{
 			LastConfig: &common.LastConfig{Index: rl.Height()},
 		}),
 	})
-	nextBlock.Metadata.Metadata[common.BlockMetadataIndex_LAST_CONFIG] = protoutil.MarshalOrPanic(&common.Metadata{
+	configBlock.Metadata.Metadata[common.BlockMetadataIndex_LAST_CONFIG] = protoutil.MarshalOrPanic(&common.Metadata{
 		Value: protoutil.MarshalOrPanic(&common.LastConfig{Index: rl.Height()}),
 	})
-	err = rl.Append(nextBlock)
+	err = rl.Append(configBlock)
 	require.NoError(t, err)
 
-	lastConf = extractSysChanLastConfig(rlf, genesisBlock)
-	require.NotNil(t, lastConf)
+	lastConf = extractSystemChannel(rlf, cryptoProvider)
+	require.NotNil(t, lastConf, "get system channel last config block")
 	require.Equal(t, uint64(1), lastConf.Header.Number)
 }