diff --git a/build/gobind-pinecone/monolith.go b/build/gobind-pinecone/monolith.go
index 46fe24ceb..47ca20dbd 100644
--- a/build/gobind-pinecone/monolith.go
+++ b/build/gobind-pinecone/monolith.go
@@ -260,7 +260,7 @@ func (m *DendriteMonolith) Start() {
 
 	prefix := hex.EncodeToString(pk)
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = gomatrixserverlib.ServerName(hex.EncodeToString(pk))
 	cfg.Global.PrivateKey = sk
 	cfg.Global.KeyID = gomatrixserverlib.KeyID(signing.KeyID)
diff --git a/build/gobind-yggdrasil/monolith.go b/build/gobind-yggdrasil/monolith.go
index fcfb7a255..bde9fbdfa 100644
--- a/build/gobind-yggdrasil/monolith.go
+++ b/build/gobind-yggdrasil/monolith.go
@@ -82,7 +82,7 @@ func (m *DendriteMonolith) Start() {
 	m.YggdrasilNode = ygg
 
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = gomatrixserverlib.ServerName(ygg.DerivedServerName())
 	cfg.Global.PrivateKey = ygg.PrivateKey()
 	cfg.Global.KeyID = gomatrixserverlib.KeyID(signing.KeyID)
diff --git a/clientapi/routing/register_test.go b/clientapi/routing/register_test.go
index ea07f30be..1f615dc26 100644
--- a/clientapi/routing/register_test.go
+++ b/clientapi/routing/register_test.go
@@ -180,7 +180,7 @@ func TestValidationOfApplicationServices(t *testing.T) {
 
 	// Set up a config
 	fakeConfig := &config.Dendrite{}
-	fakeConfig.Defaults()
+	fakeConfig.Defaults(true)
 	fakeConfig.Global.ServerName = "localhost"
 	fakeConfig.ClientAPI.Derived.ApplicationServices = []config.ApplicationService{fakeApplicationService}
 
diff --git a/cmd/dendrite-demo-libp2p/main.go b/cmd/dendrite-demo-libp2p/main.go
index 6a1428d57..d518d1586 100644
--- a/cmd/dendrite-demo-libp2p/main.go
+++ b/cmd/dendrite-demo-libp2p/main.go
@@ -119,7 +119,7 @@ func main() {
 	}
 
 	cfg := config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = "p2p"
 	cfg.Global.PrivateKey = privKey
 	cfg.Global.KeyID = gomatrixserverlib.KeyID(fmt.Sprintf("ed25519:%s", *instanceName))
diff --git a/cmd/dendrite-demo-pinecone/main.go b/cmd/dendrite-demo-pinecone/main.go
index 9afa53a6c..2b56ef35d 100644
--- a/cmd/dendrite-demo-pinecone/main.go
+++ b/cmd/dendrite-demo-pinecone/main.go
@@ -142,7 +142,7 @@ func main() {
 	}
 
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = gomatrixserverlib.ServerName(hex.EncodeToString(pk))
 	cfg.Global.PrivateKey = sk
 	cfg.Global.KeyID = gomatrixserverlib.KeyID(signing.KeyID)
diff --git a/cmd/dendrite-demo-yggdrasil/main.go b/cmd/dendrite-demo-yggdrasil/main.go
index 2663aabb0..1e0a7d03e 100644
--- a/cmd/dendrite-demo-yggdrasil/main.go
+++ b/cmd/dendrite-demo-yggdrasil/main.go
@@ -73,7 +73,7 @@ func main() {
 	*/
 
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = gomatrixserverlib.ServerName(ygg.DerivedServerName())
 	cfg.Global.PrivateKey = ygg.PrivateKey()
 	cfg.Global.KeyID = gomatrixserverlib.KeyID(signing.KeyID)
diff --git a/cmd/dendritejs-pinecone/main.go b/cmd/dendritejs-pinecone/main.go
index a430f82ae..10ba07172 100644
--- a/cmd/dendritejs-pinecone/main.go
+++ b/cmd/dendritejs-pinecone/main.go
@@ -161,7 +161,7 @@ func startup() {
 	pSessions := pineconeSessions.NewSessions(logger, pRouter)
 
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.UserAPI.AccountDatabase.ConnectionString = "file:/idb/dendritejs_account.db"
 	cfg.AppServiceAPI.Database.ConnectionString = "file:/idb/dendritejs_appservice.db"
 	cfg.UserAPI.DeviceDatabase.ConnectionString = "file:/idb/dendritejs_device.db"
diff --git a/cmd/dendritejs/main.go b/cmd/dendritejs/main.go
index 9bb1f24e4..969581168 100644
--- a/cmd/dendritejs/main.go
+++ b/cmd/dendritejs/main.go
@@ -164,7 +164,7 @@ func createP2PNode(privKey ed25519.PrivateKey) (serverName string, node *go_http
 
 func main() {
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.UserAPI.AccountDatabase.ConnectionString = "file:/idb/dendritejs_account.db"
 	cfg.AppServiceAPI.Database.ConnectionString = "file:/idb/dendritejs_appservice.db"
 	cfg.UserAPI.DeviceDatabase.ConnectionString = "file:/idb/dendritejs_device.db"
diff --git a/cmd/generate-config/main.go b/cmd/generate-config/main.go
index a0407b732..ff91e753f 100644
--- a/cmd/generate-config/main.go
+++ b/cmd/generate-config/main.go
@@ -17,7 +17,7 @@ func main() {
 	flag.Parse()
 
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	if *serverName != "" {
 		cfg.Global.ServerName = gomatrixserverlib.ServerName(*serverName)
 	}
diff --git a/federationapi/federationapi_keys_test.go b/federationapi/federationapi_keys_test.go
index a0051e199..fb4307aa7 100644
--- a/federationapi/federationapi_keys_test.go
+++ b/federationapi/federationapi_keys_test.go
@@ -71,7 +71,7 @@ func TestMain(m *testing.M) {
 		// Draw up just enough Dendrite config for the server key
 		// API to work.
 		cfg := &config.Dendrite{}
-		cfg.Defaults()
+		cfg.Defaults(true)
 		cfg.Global.ServerName = gomatrixserverlib.ServerName(s.name)
 		cfg.Global.PrivateKey = testPriv
 		cfg.Global.Kafka.UseNaffka = true
diff --git a/federationapi/federationapi_test.go b/federationapi/federationapi_test.go
index 0c5ee740f..8b5bdd034 100644
--- a/federationapi/federationapi_test.go
+++ b/federationapi/federationapi_test.go
@@ -19,7 +19,7 @@ import (
 func TestRoomsV3URLEscapeDoNot404(t *testing.T) {
 	_, privKey, _ := ed25519.GenerateKey(nil)
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.KeyID = gomatrixserverlib.KeyID("ed25519:auto")
 	cfg.Global.ServerName = gomatrixserverlib.ServerName("localhost")
 	cfg.Global.PrivateKey = privKey
diff --git a/internal/test/config.go b/internal/test/config.go
index 6281e7f66..826d2ce00 100644
--- a/internal/test/config.go
+++ b/internal/test/config.go
@@ -50,7 +50,7 @@ const (
 // Generates new matrix and TLS keys for the server.
 func MakeConfig(configDir, kafkaURI, database, host string, startPort int) (*config.Dendrite, int, error) {
 	var cfg config.Dendrite
-	cfg.Defaults()
+	cfg.Defaults(true)
 
 	port := startPort
 	assignAddress := func() config.HTTPAddress {
diff --git a/roomserver/roomserver_test.go b/roomserver/roomserver_test.go
index 8d92d8d8b..40e8e92d1 100644
--- a/roomserver/roomserver_test.go
+++ b/roomserver/roomserver_test.go
@@ -158,7 +158,7 @@ func mustLoadRawEvents(t *testing.T, ver gomatrixserverlib.RoomVersion, events [
 func mustCreateRoomserverAPI(t *testing.T) (api.RoomserverInternalAPI, *dummyProducer) {
 	t.Helper()
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = testOrigin
 	cfg.Global.Kafka.UseNaffka = true
 	cfg.RoomServer.Database = config.DatabaseOptions{
diff --git a/setup/config/config.go b/setup/config/config.go
index 44a67c2a3..404b7178b 100644
--- a/setup/config/config.go
+++ b/setup/config/config.go
@@ -210,7 +210,7 @@ func loadConfig(
 	monolithic bool,
 ) (*Dendrite, error) {
 	var c Dendrite
-	c.Defaults()
+	c.Defaults(false)
 
 	var err error
 	if err = yaml.Unmarshal(configData, &c); err != nil {
@@ -291,20 +291,20 @@ func (config *Dendrite) Derive() error {
 }
 
 // SetDefaults sets default config values if they are not explicitly set.
-func (c *Dendrite) Defaults() {
+func (c *Dendrite) Defaults(generate bool) {
 	c.Version = 1
 
-	c.Global.Defaults()
-	c.ClientAPI.Defaults()
-	c.EDUServer.Defaults()
-	c.FederationAPI.Defaults()
-	c.KeyServer.Defaults()
-	c.MediaAPI.Defaults()
-	c.RoomServer.Defaults()
-	c.SyncAPI.Defaults()
-	c.UserAPI.Defaults()
-	c.AppServiceAPI.Defaults()
-	c.MSCs.Defaults()
+	c.Global.Defaults(generate)
+	c.ClientAPI.Defaults(generate)
+	c.EDUServer.Defaults(generate)
+	c.FederationAPI.Defaults(generate)
+	c.KeyServer.Defaults(generate)
+	c.MediaAPI.Defaults(generate)
+	c.RoomServer.Defaults(generate)
+	c.SyncAPI.Defaults(generate)
+	c.UserAPI.Defaults(generate)
+	c.AppServiceAPI.Defaults(generate)
+	c.MSCs.Defaults(generate)
 
 	c.Wiring()
 }
diff --git a/setup/config/config_appservice.go b/setup/config/config_appservice.go
index 9bd8a1b51..4f6553f10 100644
--- a/setup/config/config_appservice.go
+++ b/setup/config/config_appservice.go
@@ -40,11 +40,13 @@ type AppServiceAPI struct {
 	ConfigFiles []string `yaml:"config_files"`
 }
 
-func (c *AppServiceAPI) Defaults() {
+func (c *AppServiceAPI) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7777"
 	c.InternalAPI.Connect = "http://localhost:7777"
 	c.Database.Defaults(5)
-	c.Database.ConnectionString = "file:appservice.db"
+	if generate {
+		c.Database.ConnectionString = "file:appservice.db"
+	}
 }
 
 func (c *AppServiceAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
diff --git a/setup/config/config_clientapi.go b/setup/config/config_clientapi.go
index c7cb9c33e..75f5e3df3 100644
--- a/setup/config/config_clientapi.go
+++ b/setup/config/config_clientapi.go
@@ -41,7 +41,7 @@ type ClientAPI struct {
 	MSCs *MSCs `yaml:"mscs"`
 }
 
-func (c *ClientAPI) Defaults() {
+func (c *ClientAPI) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7771"
 	c.InternalAPI.Connect = "http://localhost:7771"
 	c.ExternalAPI.Listen = "http://[::]:8071"
diff --git a/setup/config/config_eduserver.go b/setup/config/config_eduserver.go
index a2ff36973..e7ed36aa0 100644
--- a/setup/config/config_eduserver.go
+++ b/setup/config/config_eduserver.go
@@ -6,7 +6,7 @@ type EDUServer struct {
 	InternalAPI InternalAPIOptions `yaml:"internal_api"`
 }
 
-func (c *EDUServer) Defaults() {
+func (c *EDUServer) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7778"
 	c.InternalAPI.Connect = "http://localhost:7778"
 }
diff --git a/setup/config/config_federationapi.go b/setup/config/config_federationapi.go
index cd5015fda..4f5f49de8 100644
--- a/setup/config/config_federationapi.go
+++ b/setup/config/config_federationapi.go
@@ -39,12 +39,14 @@ type FederationAPI struct {
 	PreferDirectFetch bool `yaml:"prefer_direct_fetch"`
 }
 
-func (c *FederationAPI) Defaults() {
+func (c *FederationAPI) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7772"
 	c.InternalAPI.Connect = "http://localhost:7772"
 	c.ExternalAPI.Listen = "http://[::]:8072"
 	c.Database.Defaults(10)
-	c.Database.ConnectionString = "file:federationapi.db"
+	if generate {
+		c.Database.ConnectionString = "file:federationapi.db"
+	}
 
 	c.FederationMaxRetries = 16
 	c.DisableTLSValidation = false
diff --git a/setup/config/config_global.go b/setup/config/config_global.go
index d5d9f7f51..20ee6d37f 100644
--- a/setup/config/config_global.go
+++ b/setup/config/config_global.go
@@ -59,15 +59,17 @@ type Global struct {
 	DNSCache DNSCacheOptions `yaml:"dns_cache"`
 }
 
-func (c *Global) Defaults() {
-	c.ServerName = "localhost"
-	c.PrivateKeyPath = "matrix_key.pem"
-	_, c.PrivateKey, _ = ed25519.GenerateKey(rand.New(rand.NewSource(0)))
-	c.KeyID = "ed25519:auto"
+func (c *Global) Defaults(generate bool) {
+	if generate {
+		c.ServerName = "localhost"
+		c.PrivateKeyPath = "matrix_key.pem"
+		_, c.PrivateKey, _ = ed25519.GenerateKey(rand.New(rand.NewSource(0)))
+		c.KeyID = "ed25519:auto"
+	}
 	c.KeyValidityPeriod = time.Hour * 24 * 7
 
-	c.Kafka.Defaults()
-	c.Metrics.Defaults()
+	c.Kafka.Defaults(generate)
+	c.Metrics.Defaults(generate)
 	c.DNSCache.Defaults()
 	c.Sentry.Defaults()
 }
@@ -110,10 +112,12 @@ type Metrics struct {
 	} `yaml:"basic_auth"`
 }
 
-func (c *Metrics) Defaults() {
+func (c *Metrics) Defaults(generate bool) {
 	c.Enabled = false
-	c.BasicAuth.Username = "metrics"
-	c.BasicAuth.Password = "metrics"
+	if generate {
+		c.BasicAuth.Username = "metrics"
+		c.BasicAuth.Password = "metrics"
+	}
 }
 
 func (c *Metrics) Verify(configErrs *ConfigErrors, isMonolith bool) {
diff --git a/setup/config/config_kafka.go b/setup/config/config_kafka.go
index 361914287..5a61f17eb 100644
--- a/setup/config/config_kafka.go
+++ b/setup/config/config_kafka.go
@@ -34,11 +34,13 @@ func (k *Kafka) TopicFor(name string) string {
 	return fmt.Sprintf("%s%s", k.TopicPrefix, name)
 }
 
-func (c *Kafka) Defaults() {
+func (c *Kafka) Defaults(generate bool) {
 	c.UseNaffka = true
 	c.Database.Defaults(10)
-	c.Addresses = []string{"localhost:2181"}
-	c.Database.ConnectionString = DataSource("file:naffka.db")
+	if generate {
+		c.Addresses = []string{"localhost:2181"}
+		c.Database.ConnectionString = DataSource("file:naffka.db")
+	}
 	c.TopicPrefix = "Dendrite"
 
 	maxBytes := 1024 * 1024 * 8 // about 8MB
diff --git a/setup/config/config_keyserver.go b/setup/config/config_keyserver.go
index 62a30dbb9..6180ccbc8 100644
--- a/setup/config/config_keyserver.go
+++ b/setup/config/config_keyserver.go
@@ -8,11 +8,13 @@ type KeyServer struct {
 	Database DatabaseOptions `yaml:"database"`
 }
 
-func (c *KeyServer) Defaults() {
+func (c *KeyServer) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7779"
 	c.InternalAPI.Connect = "http://localhost:7779"
 	c.Database.Defaults(10)
-	c.Database.ConnectionString = "file:keyserver.db"
+	if generate {
+		c.Database.ConnectionString = "file:keyserver.db"
+	}
 }
 
 func (c *KeyServer) Verify(configErrs *ConfigErrors, isMonolith bool) {
diff --git a/setup/config/config_mediaapi.go b/setup/config/config_mediaapi.go
index c55978e11..9a7d84969 100644
--- a/setup/config/config_mediaapi.go
+++ b/setup/config/config_mediaapi.go
@@ -38,16 +38,18 @@ type MediaAPI struct {
 // DefaultMaxFileSizeBytes defines the default file size allowed in transfers
 var DefaultMaxFileSizeBytes = FileSizeBytes(10485760)
 
-func (c *MediaAPI) Defaults() {
+func (c *MediaAPI) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7774"
 	c.InternalAPI.Connect = "http://localhost:7774"
 	c.ExternalAPI.Listen = "http://[::]:8074"
 	c.Database.Defaults(5)
-	c.Database.ConnectionString = "file:mediaapi.db"
+	if generate {
+		c.Database.ConnectionString = "file:mediaapi.db"
+		c.BasePath = "./media_store"
+	}
 
 	c.MaxFileSizeBytes = &DefaultMaxFileSizeBytes
 	c.MaxThumbnailGenerators = 10
-	c.BasePath = "./media_store"
 }
 
 func (c *MediaAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
diff --git a/setup/config/config_mscs.go b/setup/config/config_mscs.go
index a94e5dc56..66a4c80c9 100644
--- a/setup/config/config_mscs.go
+++ b/setup/config/config_mscs.go
@@ -13,9 +13,11 @@ type MSCs struct {
 	Database DatabaseOptions `yaml:"database"`
 }
 
-func (c *MSCs) Defaults() {
+func (c *MSCs) Defaults(generate bool) {
 	c.Database.Defaults(5)
-	c.Database.ConnectionString = "file:mscs.db"
+	if generate {
+		c.Database.ConnectionString = "file:mscs.db"
+	}
 }
 
 // Enabled returns true if the given msc is enabled. Should in the form 'msc12345'.
diff --git a/setup/config/config_roomserver.go b/setup/config/config_roomserver.go
index ffb9b5f9d..73abb4f47 100644
--- a/setup/config/config_roomserver.go
+++ b/setup/config/config_roomserver.go
@@ -8,11 +8,13 @@ type RoomServer struct {
 	Database DatabaseOptions `yaml:"database"`
 }
 
-func (c *RoomServer) Defaults() {
+func (c *RoomServer) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7770"
 	c.InternalAPI.Connect = "http://localhost:7770"
 	c.Database.Defaults(10)
-	c.Database.ConnectionString = "file:roomserver.db"
+	if generate {
+		c.Database.ConnectionString = "file:roomserver.db"
+	}
 }
 
 func (c *RoomServer) Verify(configErrs *ConfigErrors, isMonolith bool) {
diff --git a/setup/config/config_syncapi.go b/setup/config/config_syncapi.go
index 4b9bfb161..dc813cb7d 100644
--- a/setup/config/config_syncapi.go
+++ b/setup/config/config_syncapi.go
@@ -11,12 +11,14 @@ type SyncAPI struct {
 	RealIPHeader string `yaml:"real_ip_header"`
 }
 
-func (c *SyncAPI) Defaults() {
+func (c *SyncAPI) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7773"
 	c.InternalAPI.Connect = "http://localhost:7773"
 	c.ExternalAPI.Listen = "http://localhost:8073"
 	c.Database.Defaults(10)
-	c.Database.ConnectionString = "file:syncapi.db"
+	if generate {
+		c.Database.ConnectionString = "file:syncapi.db"
+	}
 }
 
 func (c *SyncAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
diff --git a/setup/config/config_userapi.go b/setup/config/config_userapi.go
index 2bf1be3dd..b2cde2e96 100644
--- a/setup/config/config_userapi.go
+++ b/setup/config/config_userapi.go
@@ -23,13 +23,15 @@ type UserAPI struct {
 
 const DefaultOpenIDTokenLifetimeMS = 3600000 // 60 minutes
 
-func (c *UserAPI) Defaults() {
+func (c *UserAPI) Defaults(generate bool) {
 	c.InternalAPI.Listen = "http://localhost:7781"
 	c.InternalAPI.Connect = "http://localhost:7781"
 	c.AccountDatabase.Defaults(10)
 	c.DeviceDatabase.Defaults(10)
-	c.AccountDatabase.ConnectionString = "file:userapi_accounts.db"
-	c.DeviceDatabase.ConnectionString = "file:userapi_devices.db"
+	if generate {
+		c.AccountDatabase.ConnectionString = "file:userapi_accounts.db"
+		c.DeviceDatabase.ConnectionString = "file:userapi_devices.db"
+	}
 	c.BCryptCost = bcrypt.DefaultCost
 	c.OpenIDTokenLifetimeMS = DefaultOpenIDTokenLifetimeMS
 }
diff --git a/setup/mscs/msc2836/msc2836_test.go b/setup/mscs/msc2836/msc2836_test.go
index 5572d107f..18ab08be0 100644
--- a/setup/mscs/msc2836/msc2836_test.go
+++ b/setup/mscs/msc2836/msc2836_test.go
@@ -545,7 +545,7 @@ func (r *testRoomserverAPI) QueryMembershipForUser(ctx context.Context, req *roo
 func injectEvents(t *testing.T, userAPI userapi.UserInternalAPI, rsAPI roomserver.RoomserverInternalAPI, events []*gomatrixserverlib.HeaderedEvent) *mux.Router {
 	t.Helper()
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = "localhost"
 	cfg.MSCs.Database.ConnectionString = "file:msc2836_test.db"
 	cfg.MSCs.MSCs = []string{"msc2836"}
diff --git a/setup/mscs/msc2946/msc2946_test.go b/setup/mscs/msc2946/msc2946_test.go
index 43d605573..441892f3e 100644
--- a/setup/mscs/msc2946/msc2946_test.go
+++ b/setup/mscs/msc2946/msc2946_test.go
@@ -411,7 +411,7 @@ func (r *testRoomserverAPI) QueryCurrentState(ctx context.Context, req *roomserv
 func injectEvents(t *testing.T, userAPI userapi.UserInternalAPI, rsAPI roomserver.RoomserverInternalAPI, events []*gomatrixserverlib.HeaderedEvent) *mux.Router {
 	t.Helper()
 	cfg := &config.Dendrite{}
-	cfg.Defaults()
+	cfg.Defaults(true)
 	cfg.Global.ServerName = "localhost"
 	cfg.MSCs.Database.ConnectionString = "file:msc2946_test.db"
 	cfg.MSCs.MSCs = []string{"msc2946"}