diff --git a/internal/logger/markdown_logger.go b/internal/logger/markdown_logger.go
index d39d850f..6a432c72 100644
--- a/internal/logger/markdown_logger.go
+++ b/internal/logger/markdown_logger.go
@@ -134,8 +134,22 @@ func (ml *MarkdownLogger) Log(level LogLevel, category, format string, args ...i
 	isPreformatted := strings.HasPrefix(message, "**") && (strings.Contains(message, "→") || strings.Contains(message, "←"))
 
 	if isPreformatted {
-		// Pre-formatted content (like RPC messages) - just add bullet and emoji
-		logLine = fmt.Sprintf("- %s %s %s\n", emoji, category, message)
+		// Pre-formatted content (like RPC messages) - add bullet and emoji
+		// If the message contains newlines (e.g., JSON code blocks), indent them properly
+		if strings.Contains(message, "\n") {
+			// Split the message into lines and indent continuation lines with 2 spaces
+			lines := strings.Split(message, "\n")
+			firstLine := lines[0]
+			// Start with the first line
+			logLine = fmt.Sprintf("- %s %s %s\n", emoji, category, firstLine)
+			// Add remaining lines with proper indentation (2 spaces to nest under bullet)
+			for i := 1; i < len(lines); i++ {
+				logLine += "  " + lines[i] + "\n"
+			}
+		} else {
+			// Single-line pre-formatted message
+			logLine = fmt.Sprintf("- %s %s %s\n", emoji, category, message)
+		}
 	} else if strings.Contains(message, "\n") || strings.Contains(message, "command=") || strings.Contains(message, "args=") {
 		// Multi-line or technical content - use code block
 		logLine = fmt.Sprintf("- %s **%s**\n  ```\n  %s\n  ```\n", emoji, category, message)
diff --git a/internal/logger/markdown_logger_test.go b/internal/logger/markdown_logger_test.go
index d769e501..8296d091 100644
--- a/internal/logger/markdown_logger_test.go
+++ b/internal/logger/markdown_logger_test.go
@@ -304,9 +304,16 @@ func TestMarkdownLoggerRPCFormatting(t *testing.T) {
 	assert.True(t, strings.Contains(logContent, "- 🔍 rpc **github**→`tools/list`"), "RPC message should be on single line without extra code block wrapping")
 
 	// Check that RPC messages with JSON blocks are properly formatted
-	// The title should be on one line, followed by the JSON block
+	// The title should be on one line, followed by the JSON block INDENTED with 2 spaces
 	assert.True(t, strings.Contains(logContent, "- 🔍 rpc **safeoutputs**→`tools/call`"), "RPC message with JSON should have title on single line")
 
+	// Verify that JSON code block lines are properly indented under the bullet point
+	// The empty line after the first line should be indented
+	assert.True(t, strings.Contains(logContent, "- 🔍 rpc **safeoutputs**→`tools/call`\n  \n  ```json"), "JSON code block should be indented with 2 spaces")
+
+	// Verify the closing code fence is also indented
+	assert.True(t, strings.Contains(logContent, "  ```"), "Closing code fence should be indented")
+
 	// Regular multi-line messages should still use code blocks
 	assert.True(t, strings.Contains(logContent, "- ✓ **backend**\n  ```\n  command="), "Regular multi-line messages should still use code blocks")