diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2ce9161b127d..945e13e139a0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -85,6 +85,9 @@ Main (unreleased)
 - Fix an issue with static integrations-next marshaling where non singletons
   would cause `/-/config` to fail to marshal. (@erikbaranowski)
 
+- Fix an issue where agent logs are emitted before the logging format
+  is correctly determined. (@hainenber)
+
 - Fix divide-by-zero issue when sharding targets. (@hainenber) 
 
 - Fix bug where custom headers were not actually being set in loki client. (@captncraig)
diff --git a/cmd/internal/flowmode/cmd_run.go b/cmd/internal/flowmode/cmd_run.go
index fb3c5a235f52..263ed5ecdc88 100644
--- a/cmd/internal/flowmode/cmd_run.go
+++ b/cmd/internal/flowmode/cmd_run.go
@@ -162,7 +162,8 @@ func (fr *flowRun) Run(configPath string) error {
 		return fmt.Errorf("path argument not provided")
 	}
 
-	l, err := logging.New(os.Stderr, logging.DefaultOptions)
+	// Buffer logs until log format has been determined
+	l, err := logging.NewDeferred(os.Stderr)
 	if err != nil {
 		return fmt.Errorf("building logger: %w", err)
 	}
diff --git a/pkg/flow/logging/logger.go b/pkg/flow/logging/logger.go
index 0b80e88336ef..da0046a281af 100644
--- a/pkg/flow/logging/logger.go
+++ b/pkg/flow/logging/logger.go
@@ -23,6 +23,10 @@ type EnabledAware interface {
 type Logger struct {
 	inner io.Writer // Writer passed to New.
 
+	bufferMut    sync.RWMutex
+	buffer       [][]interface{} // Store logs before correctly determine the log format
+	hasLogFormat bool            // Confirmation whether log format has been determined
+
 	level   *slog.LevelVar // Current configured level.
 	format  *formatVar     // Current configured format.
 	writer  *writerVar     // Current configured multiwriter (inner + write_to).
@@ -47,6 +51,9 @@ func New(w io.Writer, o Options) (*Logger, error) {
 	l := &Logger{
 		inner: w,
 
+		buffer:       [][]interface{}{},
+		hasLogFormat: false,
+
 		level:  &leveler,
 		format: &format,
 		writer: &writer,
@@ -60,6 +67,35 @@ func New(w io.Writer, o Options) (*Logger, error) {
 	if err := l.Update(o); err != nil {
 		return nil, err
 	}
+
+	return l, nil
+}
+
+// NewDeferred creates a new logger with the default log level and format.
+// The logger is not updated during initialization.
+func NewDeferred(w io.Writer) (*Logger, error) {
+	var (
+		leveler slog.LevelVar
+		format  formatVar
+		writer  writerVar
+	)
+
+	l := &Logger{
+		inner: w,
+
+		buffer:       [][]interface{}{},
+		hasLogFormat: false,
+
+		level:  &leveler,
+		format: &format,
+		writer: &writer,
+		handler: &handler{
+			w:         &writer,
+			leveler:   &leveler,
+			formatter: &format,
+		},
+	}
+
 	return l, nil
 }
 
@@ -69,9 +105,12 @@ func (l *Logger) Handler() slog.Handler { return l.handler }
 
 // Update re-configures the options used for the logger.
 func (l *Logger) Update(o Options) error {
+	l.bufferMut.Lock()
+	defer l.bufferMut.Unlock()
+
 	switch o.Format {
 	case FormatLogfmt, FormatJSON:
-		// no-op
+		l.hasLogFormat = true
 	default:
 		return fmt.Errorf("unrecognized log format %q", o.Format)
 	}
@@ -85,11 +124,35 @@ func (l *Logger) Update(o Options) error {
 	}
 	l.writer.Set(newWriter)
 
+	// Print out the buffered logs since we determined the log format already
+	for _, bufferedLogChunk := range l.buffer {
+		if err := slogadapter.GoKit(l.handler).Log(bufferedLogChunk...); err != nil {
+			return err
+		}
+	}
+	l.buffer = nil
+
 	return nil
 }
 
 // Log implements log.Logger.
 func (l *Logger) Log(kvps ...interface{}) error {
+	// Buffer logs before confirming log format is configured in `logging` block
+	l.bufferMut.RLock()
+	if !l.hasLogFormat {
+		l.bufferMut.RUnlock()
+		l.bufferMut.Lock()
+		// Check hasLogFormat again; could have changed since the unlock.
+		if !l.hasLogFormat {
+			l.buffer = append(l.buffer, kvps)
+			l.bufferMut.Unlock()
+			return nil
+		}
+		l.bufferMut.Unlock()
+	} else {
+		l.bufferMut.RUnlock()
+	}
+
 	// NOTE(rfratto): this method is a temporary shim while log/slog is still
 	// being adopted throughout the codebase.
 	return slogadapter.GoKit(l.handler).Log(kvps...)