diff --git a/src/ocrmypdf/api.py b/src/ocrmypdf/api.py
index d4680a76..16978899 100644
--- a/src/ocrmypdf/api.py
+++ b/src/ocrmypdf/api.py
@@ -70,6 +70,49 @@ PathOrIO = BinaryIO | StrPath
 _api_lock = threading.Lock()
 
 
+def setup_plugin_infrastructure(
+    plugins: Sequence[Path | str] | None = None,
+    plugin_manager: pluggy.PluginManager | None = None,
+) -> pluggy.PluginManager:
+    """Set up plugin infrastructure with proper initialization.
+    
+    This function handles:
+    1. Creating or validating the plugin manager
+    2. Calling plugin initialization hooks
+    3. Setting up any future plugin registries (Phase 2)
+    
+    Args:
+        plugins: List of plugin paths/names to load
+        plugin_manager: Existing plugin manager (if any)
+        
+    Returns:
+        Properly initialized plugin manager
+        
+    Raises:
+        ValueError: If both plugins and plugin_manager are provided
+    """
+    if plugins and plugin_manager:
+        raise ValueError("plugins= and plugin_manager are mutually exclusive")
+    
+    if not plugins:
+        plugins = []
+    elif isinstance(plugins, (str, Path)):
+        plugins = [plugins]
+    else:
+        plugins = list(plugins)
+    
+    # Create plugin manager if not provided
+    if not plugin_manager:
+        plugin_manager = get_plugin_manager(plugins)
+    
+    # Initialize plugins (this was missing in the API path)
+    plugin_manager.hook.initialize(plugin_manager=plugin_manager)  # pylint: disable=no-member
+    
+    # Future: Initialize plugin option registry here (Phase 2)
+    
+    return plugin_manager
+
+
 class Verbosity(IntEnum):
     """Verbosity level for configure_logging."""
 
@@ -363,8 +406,14 @@ def ocr(  # noqa: D417
 
     parser = get_parser()
     with _api_lock:
-        if not plugin_manager:
-            plugin_manager = get_plugin_manager(plugins)
+        # Set up plugin infrastructure with proper initialization
+        plugin_manager = setup_plugin_infrastructure(
+            plugins=plugins, 
+            plugin_manager=plugin_manager
+        )
+        
+        # Get parser and let plugins add their options
+        parser = get_parser()
         plugin_manager.hook.add_options(parser=parser)  # pylint: disable=no-member
 
         if 'verbose' in kwargs:
@@ -490,8 +539,12 @@ def _pdf_to_hocr(  # noqa: D417
             extra_attrs[key] = options_kwargs.pop(key)
 
     with _api_lock:
-        if not plugin_manager:
-            plugin_manager = get_plugin_manager(plugins)
+        # Set up plugin infrastructure with proper initialization
+        plugin_manager = setup_plugin_infrastructure(
+            plugins=plugins,
+            plugin_manager=plugin_manager
+        )
+        
         plugin_manager.hook.add_options(parser=get_parser())  # pylint: disable=no-member
 
         # Create OCROptions directly
@@ -589,8 +642,12 @@ def _hocr_to_ocr_pdf(  # noqa: D417
             extra_attrs[key] = options_kwargs.pop(key)
 
     with _api_lock:
-        if not plugin_manager:
-            plugin_manager = get_plugin_manager(plugins)
+        # Set up plugin infrastructure with proper initialization  
+        plugin_manager = setup_plugin_infrastructure(
+            plugins=plugins,
+            plugin_manager=plugin_manager
+        )
+        
         plugin_manager.hook.add_options(parser=get_parser())  # pylint: disable=no-member
 
         # Create OCROptions directly
@@ -620,4 +677,5 @@ __all__ = [
     'ocr',
     'run_pipeline',
     'run_pipeline_cli',
+    'setup_plugin_infrastructure',
 ]
diff --git a/src/ocrmypdf/cli.py b/src/ocrmypdf/cli.py
index f0d4430a..f7552177 100644
--- a/src/ocrmypdf/cli.py
+++ b/src/ocrmypdf/cli.py
@@ -483,13 +483,17 @@ def get_options_and_plugins(
     Returns:
         Tuple of (OCROptions, PluginManager)
     """
+    # Import here to avoid circular imports
+    from ocrmypdf.api import setup_plugin_infrastructure
+    
     # First pass: get plugins so we can register their options
     pre_options, _unused = plugins_only_parser.parse_known_args(args=args)
-    plugin_manager = get_plugin_manager(pre_options.plugins)
+    
+    # Set up plugin infrastructure with proper initialization
+    plugin_manager = setup_plugin_infrastructure(plugins=pre_options.plugins)
 
     # Get parser and let plugins add their options
     parser = get_parser()
-    plugin_manager.hook.initialize(plugin_manager=plugin_manager)  # pylint: disable=no-member
     plugin_manager.hook.add_options(parser=parser)  # pylint: disable=no-member
 
     # Parse all arguments
diff --git a/tests/conftest.py b/tests/conftest.py
index 31b5941f..5c03cd04 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -12,6 +12,7 @@ import pytest
 
 from ocrmypdf import api, pdfinfo
 from ocrmypdf._exec import unpaper
+from ocrmypdf.api import setup_plugin_infrastructure
 from ocrmypdf.cli import get_options_and_plugins
 from ocrmypdf.exceptions import ExitCode
 
@@ -164,3 +165,8 @@ def pytest_collection_modifyitems(config, items):
     for item in items:
         if "slow" in item.keywords:
             item.add_marker(skip_slow)
+
+
+def get_test_plugin_manager(plugins=None):
+    """Get a properly initialized plugin manager for testing."""
+    return setup_plugin_infrastructure(plugins=plugins or [])
diff --git a/tests/test_metadata.py b/tests/test_metadata.py
index 0092b602..6f31b2b7 100644
--- a/tests/test_metadata.py
+++ b/tests/test_metadata.py
@@ -16,6 +16,7 @@ from ocrmypdf._jobcontext import PdfContext
 from ocrmypdf._metadata import metadata_fixup
 from ocrmypdf._pipeline import convert_to_pdfa
 from ocrmypdf._plugin_manager import get_plugin_manager
+from ocrmypdf.api import setup_plugin_infrastructure
 from ocrmypdf.cli import get_options_and_plugins
 from ocrmypdf.exceptions import ExitCode
 from ocrmypdf.pdfa import file_claims_pdfa, generate_pdfa_ps
@@ -330,8 +331,10 @@ def test_metadata_fixup_warning(resources, outdir, caplog):
 
     copyfile(resources / 'graph.pdf', outdir / 'graph.pdf')
 
+    # Use the new setup function instead of get_plugin_manager directly
+    plugin_manager = setup_plugin_infrastructure([])
     context = PdfContext(
-        options, outdir, outdir / 'graph.pdf', None, get_plugin_manager([])
+        options, outdir, outdir / 'graph.pdf', None, plugin_manager
     )
     metadata_fixup(
         working_file=outdir / 'graph.pdf', context=context, pdf_save_settings={}
@@ -346,7 +349,7 @@ def test_metadata_fixup_warning(resources, outdir, caplog):
         graph.save(outdir / 'graph_mod.pdf')
 
     context = PdfContext(
-        options, outdir, outdir / 'graph_mod.pdf', None, get_plugin_manager([])
+        options, outdir, outdir / 'graph_mod.pdf', None, plugin_manager
     )
     metadata_fixup(
         working_file=outdir / 'graph.pdf', context=context, pdf_save_settings={}
@@ -379,8 +382,11 @@ def test_prevent_gs_invalid_xml(resources, outdir):
         ]
     )
     pdfinfo = PdfInfo(outdir / 'layers.rendered.pdf')
+    
+    # Use the new setup function
+    plugin_manager = setup_plugin_infrastructure([])
     context = PdfContext(
-        options, outdir, outdir / 'layers.rendered.pdf', pdfinfo, get_plugin_manager([])
+        options, outdir, outdir / 'layers.rendered.pdf', pdfinfo, plugin_manager
     )
 
     convert_to_pdfa(
diff --git a/tests/test_unpaper.py b/tests/test_unpaper.py
index 31425cba..83da7478 100644
--- a/tests/test_unpaper.py
+++ b/tests/test_unpaper.py
@@ -12,6 +12,7 @@ from packaging.version import Version
 
 from ocrmypdf._exec import unpaper
 from ocrmypdf._validation import check_options
+from ocrmypdf.api import setup_plugin_infrastructure
 from ocrmypdf.cli import get_options_and_plugins
 from ocrmypdf.exceptions import BadArgsError, ExitCode, MissingDependencyError