diff --git a/cmd/internal/skills/command.go b/cmd/internal/skills/command.go
index 9ccd36bb12b9..5e9b17b05a95 100644
--- a/cmd/internal/skills/command.go
+++ b/cmd/internal/skills/command.go
@@ -89,6 +89,8 @@ func run(cmd *skillsCmd, opts *internal.ToolboxOptions) error {
 		return err
 	}
 
+	opts.Cfg.SkipSourceInitialization = true
+
 	if err := os.MkdirAll(cmd.outputDir, 0755); err != nil {
 		errMsg := fmt.Errorf("error creating output directory: %w", err)
 		opts.Logger.ErrorContext(ctx, errMsg.Error())
diff --git a/internal/server/config.go b/internal/server/config.go
index efa947cefeac..eb83fe1ef2d0 100644
--- a/internal/server/config.go
+++ b/internal/server/config.go
@@ -84,6 +84,8 @@ type ServerConfig struct {
 	UserAgentMetadata []string
 	// PollInterval sets the polling frequency for configuration file updates.
 	PollInterval int
+	// SkipSourceInitialization indicates if the server should skip initializing sources.
+	SkipSourceInitialization bool
 }
 
 type logFormat string
diff --git a/internal/server/server.go b/internal/server/server.go
index d42c25b9cfcd..bbec8956aefe 100644
--- a/internal/server/server.go
+++ b/internal/server/server.go
@@ -89,6 +89,14 @@ func InitializeConfigs(ctx context.Context, cfg ServerConfig) (
 	// initialize and validate the sources from configs
 	sourcesMap := make(map[string]sources.Source)
 	for name, sc := range cfg.SourceConfigs {
+		if cfg.SkipSourceInitialization {
+			sourcesMap[name] = &sources.UninitializedSource{
+				Name:   name,
+				Config: sc,
+			}
+			continue
+		}
+
 		s, err := func() (sources.Source, error) {
 			childCtx, span := instrumentation.Tracer.Start(
 				ctx,
@@ -183,6 +191,10 @@ func InitializeConfigs(ctx context.Context, cfg ServerConfig) (
 			defer span.End()
 			t, err := tc.Initialize(sourcesMap)
 			if err != nil {
+				if cfg.SkipSourceInitialization {
+					l.WarnContext(ctx, fmt.Sprintf("unable to initialize tool %q (source skip enabled): %v", name, err))
+					return nil, nil
+				}
 				return nil, fmt.Errorf("unable to initialize tool %q: %w", name, err)
 			}
 			return t, nil
@@ -190,7 +202,9 @@ func InitializeConfigs(ctx context.Context, cfg ServerConfig) (
 		if err != nil {
 			return nil, nil, nil, nil, nil, nil, nil, err
 		}
-		toolsMap[name] = t
+		if t != nil {
+			toolsMap[name] = t
+		}
 	}
 	toolNames := make([]string, 0, len(toolsMap))
 	for name := range toolsMap {
diff --git a/internal/sources/sources.go b/internal/sources/sources.go
index 93ae0233b127..b2f213b7d045 100644
--- a/internal/sources/sources.go
+++ b/internal/sources/sources.go
@@ -16,6 +16,7 @@ package sources
 
 import (
 	"context"
+	"net/http"
 
 	"fmt"
 
@@ -65,6 +66,26 @@ type Source interface {
 	ToConfig() SourceConfig
 }
 
+// UninitializedSource is a placeholder for a source that hasn't been initialized yet.
+// It implements many common methods to satisfy type assertions during tool initialization.
+type UninitializedSource struct {
+	Name   string
+	Config SourceConfig
+}
+
+func (s *UninitializedSource) SourceType() string            { return s.Config.SourceConfigType() }
+func (s *UninitializedSource) ToConfig() SourceConfig        { return s.Config }
+func (s *UninitializedSource) HttpDefaultHeaders() map[string]string { return nil }
+func (s *UninitializedSource) HttpBaseURL() string           { return "" }
+func (s *UninitializedSource) HttpQueryParams() map[string]string { return nil }
+func (s *UninitializedSource) RunRequest(ctx context.Context, r *http.Request) (any, error) { return nil, nil }
+func (s *UninitializedSource) PostgresPool() any             { return nil }
+func (s *UninitializedSource) SQLiteDB() any                 { return nil }
+func (s *UninitializedSource) BigQueryClient() any           { return nil }
+func (s *UninitializedSource) RunSQL(ctx context.Context, stmt string, args []any) (any, error) { return nil, nil }
+func (s *UninitializedSource) GetDefaultProject() string    { return "" }
+func (s *UninitializedSource) UseClientAuthorization() bool { return false }
+
 // InitConnectionSpan adds a span for database pool connection initialization
 func InitConnectionSpan(ctx context.Context, tracer trace.Tracer, sourceType, sourceName string) (context.Context, trace.Span) {
 	ctx, span := tracer.Start(