diff --git a/config/setup.go b/config/setup.go
index 9a44cc2..f0a6ee0 100644
--- a/config/setup.go
+++ b/config/setup.go
@@ -38,6 +38,9 @@ func MergeConfig(ctx *cli.Context, config *Config) {
 	}
 
 	mergeServerConfig(ctx, &config.Server)
+	mergeGiteaConfig(ctx, &config.Gitea)
+	mergeDatabaseConfig(ctx, &config.Database)
+	mergeACMEConfig(ctx, &config.ACME)
 }
 
 func mergeServerConfig(ctx *cli.Context, config *ServerConfig) {
@@ -74,4 +77,49 @@ func mergeGiteaConfig(ctx *cli.Context, config *GiteaConfig) {
 	if ctx.IsSet("gitea-root") {
 		config.Root = ctx.String("gitea-root")
 	}
+	if ctx.IsSet("gitea-api-token") {
+		config.Token = ctx.String("gitea-api-token")
+	}
+	if ctx.IsSet("enable-lfs-support") {
+		config.LFSEnabled = ctx.Bool("enable-lfs-support")
+	}
+	if ctx.IsSet("enable-symlink-support") {
+		config.FollowSymlinks = ctx.Bool("enable-symlink-support")
+	}
+}
+
+func mergeDatabaseConfig(ctx *cli.Context, config *DatabaseConfig) {
+	if ctx.IsSet("db-type") {
+		config.Type = ctx.String("db-type")
+	}
+	if ctx.IsSet("db-conn") {
+		config.Conn = ctx.String("db-conn")
+	}
+}
+
+func mergeACMEConfig(ctx *cli.Context, config *ACMEConfig) {
+	if ctx.IsSet("acme-email") {
+		config.Email = ctx.String("acme-email")
+	}
+	if ctx.IsSet("acme-api-endpoint") {
+		config.APIEndpoint = ctx.String("acme-api-endpoint")
+	}
+	if ctx.IsSet("acme-accept-terms") {
+		config.AcceptTerms = ctx.Bool("acme-accept-terms")
+	}
+	if ctx.IsSet("acme-use-rate-limits") {
+		config.UseRateLimits = ctx.Bool("acme-use-rate-limits")
+	}
+	if ctx.IsSet("acme-eab-hmac") {
+		config.EAB_HMAC = ctx.String("acme-eab-hmac")
+	}
+	if ctx.IsSet("acme-eab-kid") {
+		config.EAB_KID = ctx.String("acme-eab-kid")
+	}
+	if ctx.IsSet("dns-provider") {
+		config.DNSProvider = ctx.String("dns-provider")
+	}
+	if ctx.IsSet("acme-account-config") {
+		config.AccountConfigFile = ctx.String("acme-account-config")
+	}
 }
diff --git a/config/setup_test.go b/config/setup_test.go
index 97704c8..c08c056 100644
--- a/config/setup_test.go
+++ b/config/setup_test.go
@@ -59,6 +59,116 @@ func TestReadConfigShouldReturnConfigFromFileWhenConfigArgPresent(t *testing.T)
 	)
 }
 
+func TestMergeConfigShouldReplaceAllExistingValuesGivenAllArgsExist(t *testing.T) {
+	runApp(
+		t,
+		func(ctx *cli.Context) error {
+			cfg := &Config{
+				LogLevel: "original",
+				Server: ServerConfig{
+					Host:               "original",
+					Port:               8080,
+					HttpPort:           80,
+					HttpServerEnabled:  false,
+					MainDomain:         "original",
+					RawDomain:          "original",
+					AllowedCorsDomains: []string{"original"},
+					BlacklistedPaths:   []string{"original"},
+				},
+				Gitea: GiteaConfig{
+					Root:           "original",
+					Token:          "original",
+					LFSEnabled:     false,
+					FollowSymlinks: false,
+				},
+				Database: DatabaseConfig{
+					Type: "original",
+					Conn: "original",
+				},
+				ACME: ACMEConfig{
+					Email:             "original",
+					APIEndpoint:       "original",
+					AcceptTerms:       false,
+					UseRateLimits:     false,
+					EAB_HMAC:          "original",
+					EAB_KID:           "original",
+					DNSProvider:       "original",
+					AccountConfigFile: "original",
+				},
+			}
+
+			MergeConfig(ctx, cfg)
+
+			expectedConfig := &Config{
+				LogLevel: "changed",
+				Server: ServerConfig{
+					Host:               "changed",
+					Port:               8443,
+					HttpPort:           443,
+					HttpServerEnabled:  true,
+					MainDomain:         "changed",
+					RawDomain:          "changed",
+					AllowedCorsDomains: []string{"changed"},
+					BlacklistedPaths:   append([]string{"changed"}, ALWAYS_BLACKLISTED_PATHS...),
+				},
+				Gitea: GiteaConfig{
+					Root:           "changed",
+					Token:          "changed",
+					LFSEnabled:     true,
+					FollowSymlinks: true,
+				},
+				Database: DatabaseConfig{
+					Type: "changed",
+					Conn: "changed",
+				},
+				ACME: ACMEConfig{
+					Email:             "changed",
+					APIEndpoint:       "changed",
+					AcceptTerms:       true,
+					UseRateLimits:     true,
+					EAB_HMAC:          "changed",
+					EAB_KID:           "changed",
+					DNSProvider:       "changed",
+					AccountConfigFile: "changed",
+				},
+			}
+
+			assert.Equal(t, expectedConfig, cfg)
+
+			return nil
+		},
+		[]string{
+			"--log-level", "changed",
+			// Server
+			"--pages-domain", "changed",
+			"--raw-domain", "changed",
+			"--allowed-cors-domains", "changed",
+			"--blacklisted-paths", "changed",
+			"--host", "changed",
+			"--port", "8443",
+			"--http-port", "443",
+			"--enable-http-server",
+			// Gitea
+			"--gitea-root", "changed",
+			"--gitea-api-token", "changed",
+			"--enable-lfs-support",
+			"--enable-symlink-support",
+			// Database
+			"--db-type", "changed",
+			"--db-conn", "changed",
+			// ACME
+			"--acme-email", "changed",
+			"--acme-api-endpoint", "changed",
+			"--acme-accept-terms",
+			"--acme-use-rate-limits",
+			"--acme-eab-hmac", "changed",
+			"--acme-eab-kid", "changed",
+			"--dns-provider", "changed",
+			"--acme-account-config", "changed",
+		},
+	)
+}
+
 func TestMergeServerConfigShouldAddDefaultBlacklistedPathsToBlacklistedPaths(t *testing.T) {
 	runApp(
 		t,
@@ -132,8 +242,8 @@ func TestMergeServerConfigShouldReplaceOnlyOneValueExistingValueGivenOnlyOneArgE
 		{args: []string{"--enable-http-server"}, callback: func(sc *ServerConfig) { sc.HttpServerEnabled = true }},
 		{args: []string{"--pages-domain", "changed"}, callback: func(sc *ServerConfig) { sc.MainDomain = "changed" }},
 		{args: []string{"--raw-domain", "changed"}, callback: func(sc *ServerConfig) { sc.RawDomain = "changed" }},
-		{args: []string{"--allowed-cors-domains", "changed"}, callback: func(sc *ServerConfig) { sc.AllowedCorsDomains = []string{"changed", "changed"} }}, // don't ask why, the cli lib always adds two strings when running all tests and one when running a single test
-		{args: []string{"--blacklisted-paths", "changed"}, callback: func(sc *ServerConfig) { sc.BlacklistedPaths = []string{"changed", "changed"} }},      // same here
+		{args: []string{"--allowed-cors-domains", "changed"}, callback: func(sc *ServerConfig) { sc.AllowedCorsDomains = []string{"changed"} }},
+		{args: []string{"--blacklisted-paths", "changed"}, callback: func(sc *ServerConfig) { sc.BlacklistedPaths = []string{"changed"} }},
 	}
 
 	for _, pair := range testValuePairs {
@@ -165,3 +275,223 @@ func TestMergeServerConfigShouldReplaceOnlyOneValueExistingValueGivenOnlyOneArgE
 		)
 	}
 }
+
+func TestMergeGiteaConfigShouldReplaceAllExistingValuesGivenAllArgsExist(t *testing.T) {
+	runApp(
+		t,
+		func(ctx *cli.Context) error {
+			cfg := &GiteaConfig{
+				Root:           "original",
+				Token:          "original",
+				LFSEnabled:     false,
+				FollowSymlinks: false,
+			}
+
+			mergeGiteaConfig(ctx, cfg)
+
+			expectedConfig := &GiteaConfig{
+				Root:           "changed",
+				Token:          "changed",
+				LFSEnabled:     true,
+				FollowSymlinks: true,
+			}
+
+			assert.Equal(t, expectedConfig, cfg)
+
+			return nil
+		},
+		[]string{
+			"--gitea-root", "changed",
+			"--gitea-api-token", "changed",
+			"--enable-lfs-support",
+			"--enable-symlink-support",
+		},
+	)
+}
+
+func TestMergeGiteaConfigShouldReplaceOnlyOneValueExistingValueGivenOnlyOneArgExists(t *testing.T) {
+	type testValuePair struct {
+		args     []string
+		callback func(*GiteaConfig)
+	}
+	testValuePairs := []testValuePair{
+		{args: []string{"--gitea-root", "changed"}, callback: func(gc *GiteaConfig) { gc.Root = "changed" }},
+		{args: []string{"--gitea-api-token", "changed"}, callback: func(gc *GiteaConfig) { gc.Token = "changed" }},
+		{args: []string{"--enable-lfs-support"}, callback: func(gc *GiteaConfig) { gc.LFSEnabled = true }},
+		{args: []string{"--enable-symlink-support"}, callback: func(gc *GiteaConfig) { gc.FollowSymlinks = true }},
+	}
+
+	for _, pair := range testValuePairs {
+		runApp(
+			t,
+			func(ctx *cli.Context) error {
+				cfg := GiteaConfig{
+					Root:           "original",
+					Token:          "original",
+					LFSEnabled:     false,
+					FollowSymlinks: false,
+				}
+
+				expectedConfig := cfg
+				pair.callback(&expectedConfig)
+
+				mergeGiteaConfig(ctx, &cfg)
+
+				assert.Equal(t, expectedConfig, cfg)
+
+				return nil
+			},
+			pair.args,
+		)
+	}
+}
+
+func TestMergeDatabaseConfigShouldReplaceAllExistingValuesGivenAllArgsExist(t *testing.T) {
+	runApp(
+		t,
+		func(ctx *cli.Context) error {
+			cfg := &DatabaseConfig{
+				Type: "original",
+				Conn: "original",
+			}
+
+			mergeDatabaseConfig(ctx, cfg)
+
+			expectedConfig := &DatabaseConfig{
+				Type: "changed",
+				Conn: "changed",
+			}
+
+			assert.Equal(t, expectedConfig, cfg)
+
+			return nil
+		},
+		[]string{
+			"--db-type", "changed",
+			"--db-conn", "changed",
+		},
+	)
+}
+
+func TestMergeDatabaseConfigShouldReplaceOnlyOneValueExistingValueGivenOnlyOneArgExists(t *testing.T) {
+	type testValuePair struct {
+		args     []string
+		callback func(*DatabaseConfig)
+	}
+	testValuePairs := []testValuePair{
+		{args: []string{"--db-type", "changed"}, callback: func(gc *DatabaseConfig) { gc.Type = "changed" }},
+		{args: []string{"--db-conn", "changed"}, callback: func(gc *DatabaseConfig) { gc.Conn = "changed" }},
+	}
+
+	for _, pair := range testValuePairs {
+		runApp(
+			t,
+			func(ctx *cli.Context) error {
+				cfg := DatabaseConfig{
+					Type: "original",
+					Conn: "original",
+				}
+
+				expectedConfig := cfg
+				pair.callback(&expectedConfig)
+
+				mergeDatabaseConfig(ctx, &cfg)
+
+				assert.Equal(t, expectedConfig, cfg)
+
+				return nil
+			},
+			pair.args,
+		)
+	}
+}
+
+func TestMergeACMEConfigShouldReplaceAllExistingValuesGivenAllArgsExist(t *testing.T) {
+	runApp(
+		t,
+		func(ctx *cli.Context) error {
+			cfg := &ACMEConfig{
+				Email:             "original",
+				APIEndpoint:       "original",
+				AcceptTerms:       false,
+				UseRateLimits:     false,
+				EAB_HMAC:          "original",
+				EAB_KID:           "original",
+				DNSProvider:       "original",
+				AccountConfigFile: "original",
+			}
+
+			mergeACMEConfig(ctx, cfg)
+
+			expectedConfig := &ACMEConfig{
+				Email:             "changed",
+				APIEndpoint:       "changed",
+				AcceptTerms:       true,
+				UseRateLimits:     true,
+				EAB_HMAC:          "changed",
+				EAB_KID:           "changed",
+				DNSProvider:       "changed",
+				AccountConfigFile: "changed",
+			}
+
+			assert.Equal(t, expectedConfig, cfg)
+
+			return nil
+		},
+		[]string{
+			"--acme-email", "changed",
+			"--acme-api-endpoint", "changed",
+			"--acme-accept-terms",
+			"--acme-use-rate-limits",
+			"--acme-eab-hmac", "changed",
+			"--acme-eab-kid", "changed",
+			"--dns-provider", "changed",
+			"--acme-account-config", "changed",
+		},
+	)
+}
+
+func TestMergeACMEConfigShouldReplaceOnlyOneValueExistingValueGivenOnlyOneArgExists(t *testing.T) {
+	type testValuePair struct {
+		args     []string
+		callback func(*ACMEConfig)
+	}
+	testValuePairs := []testValuePair{
+		{args: []string{"--acme-email", "changed"}, callback: func(gc *ACMEConfig) { gc.Email = "changed" }},
+		{args: []string{"--acme-api-endpoint", "changed"}, callback: func(gc *ACMEConfig) { gc.APIEndpoint = "changed" }},
+		{args: []string{"--acme-accept-terms"}, callback: func(gc *ACMEConfig) { gc.AcceptTerms = true }},
+		{args: []string{"--acme-use-rate-limits"}, callback: func(gc *ACMEConfig) { gc.UseRateLimits = true }},
+		{args: []string{"--acme-eab-hmac", "changed"}, callback: func(gc *ACMEConfig) { gc.EAB_HMAC = "changed" }},
+		{args: []string{"--acme-eab-kid", "changed"}, callback: func(gc *ACMEConfig) { gc.EAB_KID = "changed" }},
+		{args: []string{"--dns-provider", "changed"}, callback: func(gc *ACMEConfig) { gc.DNSProvider = "changed" }},
+		{args: []string{"--acme-account-config", "changed"}, callback: func(gc *ACMEConfig) { gc.AccountConfigFile = "changed" }},
+	}
+
+	for _, pair := range testValuePairs {
+		runApp(
+			t,
+			func(ctx *cli.Context) error {
+				cfg := ACMEConfig{
+					Email:             "original",
+					APIEndpoint:       "original",
+					AcceptTerms:       false,
+					UseRateLimits:     false,
+					EAB_HMAC:          "original",
+					EAB_KID:           "original",
+					DNSProvider:       "original",
+					AccountConfigFile: "original",
+				}
+
+				expectedConfig := cfg
+				pair.callback(&expectedConfig)
+
+				mergeACMEConfig(ctx, &cfg)
+
+				assert.Equal(t, expectedConfig, cfg)
+
+				return nil
+			},
+			pair.args,
+		)
+	}
+}