diff --git a/modules/setting/config_provider.go b/modules/setting/config_provider.go
index 3fa3f3b50b8..03f27ba203f 100644
--- a/modules/setting/config_provider.go
+++ b/modules/setting/config_provider.go
@@ -315,21 +315,25 @@ func mustMapSetting(rootCfg ConfigProvider, sectionName string, setting any) {
 	}
 }
 
-// DeprecatedWarnings contains the warning message for various deprecations, including: setting option, file/folder, etc
-var DeprecatedWarnings []string
+// StartupProblems contains the messages for various startup problems, including: setting option, file/folder, etc
+var StartupProblems []string
+
+func logStartupProblem(skip int, level log.Level, format string, args ...any) {
+	msg := fmt.Sprintf(format, args...)
+	log.Log(skip+1, level, "%s", msg)
+	StartupProblems = append(StartupProblems, msg)
+}
 
 func deprecatedSetting(rootCfg ConfigProvider, oldSection, oldKey, newSection, newKey, version string) {
 	if rootCfg.Section(oldSection).HasKey(oldKey) {
-		msg := fmt.Sprintf("Deprecated config option `[%s]` `%s` present. Use `[%s]` `%s` instead. This fallback will be/has been removed in %s", oldSection, oldKey, newSection, newKey, version)
-		log.Error("%v", msg)
-		DeprecatedWarnings = append(DeprecatedWarnings, msg)
+		logStartupProblem(1, log.ERROR, "Deprecation: config option `[%s].%s` presents, please use `[%s].%s` instead because this fallback will be/has been removed in %s", oldSection, oldKey, newSection, newKey, version)
 	}
 }
 
 // deprecatedSettingDB add a hint that the configuration has been moved to database but still kept in app.ini
 func deprecatedSettingDB(rootCfg ConfigProvider, oldSection, oldKey string) {
 	if rootCfg.Section(oldSection).HasKey(oldKey) {
-		log.Error("Deprecated `[%s]` `%s` present which has been copied to database table sys_setting", oldSection, oldKey)
+		logStartupProblem(1, log.ERROR, "Deprecation: config option `[%s].%s` presents but it won't take effect because it has been moved to admin panel -> config setting", oldSection, oldKey)
 	}
 }
 
diff --git a/modules/setting/indexer.go b/modules/setting/indexer.go
index cec364d370c..6877d70e3cf 100644
--- a/modules/setting/indexer.go
+++ b/modules/setting/indexer.go
@@ -58,7 +58,7 @@ func loadIndexerFrom(rootCfg ConfigProvider) {
 		if !filepath.IsAbs(Indexer.IssuePath) {
 			Indexer.IssuePath = filepath.ToSlash(filepath.Join(AppWorkPath, Indexer.IssuePath))
 		}
-		checkOverlappedPath("indexer.ISSUE_INDEXER_PATH", Indexer.IssuePath)
+		checkOverlappedPath("[indexer].ISSUE_INDEXER_PATH", Indexer.IssuePath)
 	} else {
 		Indexer.IssueConnStr = sec.Key("ISSUE_INDEXER_CONN_STR").MustString(Indexer.IssueConnStr)
 		if Indexer.IssueType == "meilisearch" {
diff --git a/modules/setting/oauth2.go b/modules/setting/oauth2.go
index 4d3bfd3eb60..1429a7585c9 100644
--- a/modules/setting/oauth2.go
+++ b/modules/setting/oauth2.go
@@ -168,7 +168,7 @@ func GetGeneralTokenSigningSecret() []byte {
 		}
 		if generalSigningSecret.CompareAndSwap(old, &jwtSecret) {
 			// FIXME: in main branch, the signing token should be refactored (eg: one unique for LFS/OAuth2/etc ...)
-			log.Warn("OAuth2 is not enabled, unable to use a persistent signing secret, a new one is generated, which is not persistent between restarts and cluster nodes")
+			logStartupProblem(1, log.WARN, "OAuth2 is not enabled, unable to use a persistent signing secret, a new one is generated, which is not persistent between restarts and cluster nodes")
 			return jwtSecret
 		}
 		return *generalSigningSecret.Load()
diff --git a/modules/setting/repository.go b/modules/setting/repository.go
index a332d6adb37..8656ebc7ecf 100644
--- a/modules/setting/repository.go
+++ b/modules/setting/repository.go
@@ -286,7 +286,7 @@ func loadRepositoryFrom(rootCfg ConfigProvider) {
 		RepoRootPath = filepath.Clean(RepoRootPath)
 	}
 
-	checkOverlappedPath("repository.ROOT", RepoRootPath)
+	checkOverlappedPath("[repository].ROOT", RepoRootPath)
 
 	defaultDetectedCharsetsOrder := make([]string, 0, len(Repository.DetectedCharsetsOrder))
 	for _, charset := range Repository.DetectedCharsetsOrder {
diff --git a/modules/setting/server.go b/modules/setting/server.go
index 315faaeb219..7d6ece27279 100644
--- a/modules/setting/server.go
+++ b/modules/setting/server.go
@@ -331,7 +331,7 @@ func loadServerFrom(rootCfg ConfigProvider) {
 	if !filepath.IsAbs(PprofDataPath) {
 		PprofDataPath = filepath.Join(AppWorkPath, PprofDataPath)
 	}
-	checkOverlappedPath("server.PPROF_DATA_PATH", PprofDataPath)
+	checkOverlappedPath("[server].PPROF_DATA_PATH", PprofDataPath)
 
 	landingPage := sec.Key("LANDING_PAGE").MustString("home")
 	switch landingPage {
diff --git a/modules/setting/session.go b/modules/setting/session.go
index 3cb1bfe7b50..afe63bfdb78 100644
--- a/modules/setting/session.go
+++ b/modules/setting/session.go
@@ -46,7 +46,7 @@ func loadSessionFrom(rootCfg ConfigProvider) {
 	SessionConfig.ProviderConfig = strings.Trim(sec.Key("PROVIDER_CONFIG").MustString(filepath.Join(AppDataPath, "sessions")), "\" ")
 	if SessionConfig.Provider == "file" && !filepath.IsAbs(SessionConfig.ProviderConfig) {
 		SessionConfig.ProviderConfig = filepath.Join(AppWorkPath, SessionConfig.ProviderConfig)
-		checkOverlappedPath("session.PROVIDER_CONFIG", SessionConfig.ProviderConfig)
+		checkOverlappedPath("[session].PROVIDER_CONFIG", SessionConfig.ProviderConfig)
 	}
 	SessionConfig.CookieName = sec.Key("COOKIE_NAME").MustString("i_like_gitea")
 	SessionConfig.CookiePath = AppSubURL
diff --git a/modules/setting/setting.go b/modules/setting/setting.go
index 6aca9ec6cf2..92bb0b6541b 100644
--- a/modules/setting/setting.go
+++ b/modules/setting/setting.go
@@ -235,9 +235,7 @@ var configuredPaths = make(map[string]string)
 func checkOverlappedPath(name, path string) {
 	// TODO: some paths shouldn't overlap (storage.xxx.path), while some could (data path is the base path for storage path)
 	if targetName, ok := configuredPaths[path]; ok && targetName != name {
-		msg := fmt.Sprintf("Configured path %q is used by %q and %q at the same time. The paths must be unique to prevent data loss.", path, targetName, name)
-		log.Error("%s", msg)
-		DeprecatedWarnings = append(DeprecatedWarnings, msg)
+		logStartupProblem(1, log.ERROR, "Configured path %q is used by %q and %q at the same time. The paths must be unique to prevent data loss.", path, targetName, name)
 	}
 	configuredPaths[path] = name
 }
diff --git a/modules/setting/storage.go b/modules/setting/storage.go
index f4e33a53afd..aeb61ac5134 100644
--- a/modules/setting/storage.go
+++ b/modules/setting/storage.go
@@ -240,7 +240,7 @@ func getStorageForLocal(targetSec, overrideSec ConfigSection, tp targetSecType,
 		}
 	}
 
-	checkOverlappedPath("storage."+name+".PATH", storage.Path)
+	checkOverlappedPath("[storage."+name+"].PATH", storage.Path)
 
 	return &storage, nil
 }
diff --git a/routers/web/admin/admin.go b/routers/web/admin/admin.go
index 4dc0dfdef81..e6585d8833b 100644
--- a/routers/web/admin/admin.go
+++ b/routers/web/admin/admin.go
@@ -117,11 +117,11 @@ func updateSystemStatus() {
 	sysStatus.NumGC = m.NumGC
 }
 
-func prepareDeprecatedWarningsAlert(ctx *context.Context) {
-	if len(setting.DeprecatedWarnings) > 0 {
-		content := setting.DeprecatedWarnings[0]
-		if len(setting.DeprecatedWarnings) > 1 {
-			content += fmt.Sprintf(" (and %d more)", len(setting.DeprecatedWarnings)-1)
+func prepareStartupProblemsAlert(ctx *context.Context) {
+	if len(setting.StartupProblems) > 0 {
+		content := setting.StartupProblems[0]
+		if len(setting.StartupProblems) > 1 {
+			content += fmt.Sprintf(" (and %d more)", len(setting.StartupProblems)-1)
 		}
 		ctx.Flash.Error(content, true)
 	}
@@ -136,7 +136,7 @@ func Dashboard(ctx *context.Context) {
 	updateSystemStatus()
 	ctx.Data["SysStatus"] = sysStatus
 	ctx.Data["SSH"] = setting.SSH
-	prepareDeprecatedWarningsAlert(ctx)
+	prepareStartupProblemsAlert(ctx)
 	ctx.HTML(http.StatusOK, tplDashboard)
 }
 
@@ -191,10 +191,10 @@ func DashboardPost(ctx *context.Context) {
 func SelfCheck(ctx *context.Context) {
 	ctx.Data["PageIsAdminSelfCheck"] = true
 
-	ctx.Data["DeprecatedWarnings"] = setting.DeprecatedWarnings
-	if len(setting.DeprecatedWarnings) == 0 && !setting.IsProd {
+	ctx.Data["StartupProblems"] = setting.StartupProblems
+	if len(setting.StartupProblems) == 0 && !setting.IsProd {
 		if time.Now().Unix()%2 == 0 {
-			ctx.Data["DeprecatedWarnings"] = []string{"This is a test warning message in dev mode"}
+			ctx.Data["StartupProblems"] = []string{"This is a test warning message in dev mode"}
 		}
 	}
 
diff --git a/routers/web/admin/config.go b/routers/web/admin/config.go
index 2f5f17e2013..48f80dbbf1c 100644
--- a/routers/web/admin/config.go
+++ b/routers/web/admin/config.go
@@ -165,7 +165,7 @@ func Config(ctx *context.Context) {
 
 	ctx.Data["Loggers"] = log.GetManager().DumpLoggers()
 	config.GetDynGetter().InvalidateCache()
-	prepareDeprecatedWarningsAlert(ctx)
+	prepareStartupProblemsAlert(ctx)
 
 	ctx.HTML(http.StatusOK, tplConfig)
 }
diff --git a/templates/admin/self_check.tmpl b/templates/admin/self_check.tmpl
index c100ffd5048..a6c2ac1ac9d 100644
--- a/templates/admin/self_check.tmpl
+++ b/templates/admin/self_check.tmpl
@@ -5,11 +5,11 @@
 		{{ctx.Locale.Tr "admin.self_check"}}
 	</h4>
 
-	{{if .DeprecatedWarnings}}
+	{{if .StartupProblems}}
 	<div class="ui attached segment">
 		<div class="ui warning message">
 			<div>{{ctx.Locale.Tr "admin.self_check.startup_warnings"}}</div>
-			<ul class="tw-w-full">{{range .DeprecatedWarnings}}<li>{{.}}</li>{{end}}</ul>
+			<ul class="tw-w-full">{{range .StartupProblems}}<li>{{.}}</li>{{end}}</ul>
 		</div>
 	</div>
 	{{end}}
@@ -40,7 +40,7 @@
 	</div>
 	{{end}}
 
-	{{if and (not .DeprecatedWarnings) (not .DatabaseCheckHasProblems)}}
+	{{if and (not .StartupProblems) (not .DatabaseCheckHasProblems)}}
 	<div class="ui attached segment">
 		{{ctx.Locale.Tr "admin.self_check.no_problem_found"}}
 	</div>