diff --git a/cogl/cogl-pipeline-opengl.c b/cogl/cogl-pipeline-opengl.c
index 80a7ebeaa..39db8d7c4 100644
--- a/cogl/cogl-pipeline-opengl.c
+++ b/cogl/cogl-pipeline-opengl.c
@@ -521,7 +521,8 @@ _cogl_pipeline_flush_color_blend_alpha_depth_state (
                          blend_state->blend_dst_factor_rgb));
     }
 
-  if (pipelines_difference & COGL_PIPELINE_STATE_ALPHA_FUNC)
+  if (pipelines_difference & (COGL_PIPELINE_STATE_ALPHA_FUNC |
+                              COGL_PIPELINE_STATE_ALPHA_FUNC_REFERENCE))
     {
       CoglPipeline *authority =
         _cogl_pipeline_get_authority (pipeline, COGL_PIPELINE_STATE_ALPHA_FUNC);
diff --git a/cogl/cogl-pipeline-private.h b/cogl/cogl-pipeline-private.h
index 333601a31..6e0788427 100644
--- a/cogl/cogl-pipeline-private.h
+++ b/cogl/cogl-pipeline-private.h
@@ -273,19 +273,20 @@ struct _CoglPipelineLayer
  * state changes... */
 typedef enum _CoglPipelineState
 {
-  COGL_PIPELINE_STATE_COLOR             = 1L<<0,
-  COGL_PIPELINE_STATE_BLEND_ENABLE      = 1L<<1,
-  COGL_PIPELINE_STATE_LAYERS            = 1L<<2,
+  COGL_PIPELINE_STATE_COLOR                = 1L<<0,
+  COGL_PIPELINE_STATE_BLEND_ENABLE         = 1L<<1,
+  COGL_PIPELINE_STATE_LAYERS               = 1L<<2,
 
-  COGL_PIPELINE_STATE_LIGHTING          = 1L<<3,
-  COGL_PIPELINE_STATE_ALPHA_FUNC        = 1L<<4,
-  COGL_PIPELINE_STATE_BLEND             = 1L<<5,
-  COGL_PIPELINE_STATE_USER_SHADER       = 1L<<6,
-  COGL_PIPELINE_STATE_DEPTH             = 1L<<7,
-  COGL_PIPELINE_STATE_FOG               = 1L<<8,
-  COGL_PIPELINE_STATE_POINT_SIZE        = 1L<<9,
+  COGL_PIPELINE_STATE_LIGHTING             = 1L<<3,
+  COGL_PIPELINE_STATE_ALPHA_FUNC           = 1L<<4,
+  COGL_PIPELINE_STATE_ALPHA_FUNC_REFERENCE = 1L<<5,
+  COGL_PIPELINE_STATE_BLEND                = 1L<<6,
+  COGL_PIPELINE_STATE_USER_SHADER          = 1L<<7,
+  COGL_PIPELINE_STATE_DEPTH                = 1L<<8,
+  COGL_PIPELINE_STATE_FOG                  = 1L<<9,
+  COGL_PIPELINE_STATE_POINT_SIZE           = 1L<<10,
 
-  COGL_PIPELINE_STATE_REAL_BLEND_ENABLE = 1L<<10,
+  COGL_PIPELINE_STATE_REAL_BLEND_ENABLE    = 1L<<11,
 
   COGL_PIPELINE_STATE_ALL_SPARSE =
     COGL_PIPELINE_STATE_COLOR |
@@ -293,6 +294,7 @@ typedef enum _CoglPipelineState
     COGL_PIPELINE_STATE_LAYERS |
     COGL_PIPELINE_STATE_LIGHTING |
     COGL_PIPELINE_STATE_ALPHA_FUNC |
+    COGL_PIPELINE_STATE_ALPHA_FUNC_REFERENCE |
     COGL_PIPELINE_STATE_BLEND |
     COGL_PIPELINE_STATE_USER_SHADER |
     COGL_PIPELINE_STATE_DEPTH |
@@ -310,6 +312,7 @@ typedef enum _CoglPipelineState
   COGL_PIPELINE_STATE_NEEDS_BIG_STATE =
     COGL_PIPELINE_STATE_LIGHTING |
     COGL_PIPELINE_STATE_ALPHA_FUNC |
+    COGL_PIPELINE_STATE_ALPHA_FUNC_REFERENCE |
     COGL_PIPELINE_STATE_BLEND |
     COGL_PIPELINE_STATE_USER_SHADER |
     COGL_PIPELINE_STATE_DEPTH |
diff --git a/cogl/cogl-pipeline.c b/cogl/cogl-pipeline.c
index f38450add..712bde3ce 100644
--- a/cogl/cogl-pipeline.c
+++ b/cogl/cogl-pipeline.c
@@ -1010,11 +1010,12 @@ _cogl_pipeline_copy_differences (CoglPipeline *dest,
     }
 
   if (differences & COGL_PIPELINE_STATE_ALPHA_FUNC)
-    {
-      memcpy (&big_state->alpha_state,
-              &src->big_state->alpha_state,
-              sizeof (CoglPipelineAlphaFuncState));
-    }
+    big_state->alpha_state.alpha_func =
+      src->big_state->alpha_state.alpha_func;
+
+  if (differences & COGL_PIPELINE_STATE_ALPHA_FUNC_REFERENCE)
+    big_state->alpha_state.alpha_func_reference =
+      src->big_state->alpha_state.alpha_func_reference;
 
   if (differences & COGL_PIPELINE_STATE_BLEND)
     {
@@ -3014,19 +3015,28 @@ _cogl_pipeline_lighting_state_equal (CoglPipeline *authority0,
 }
 
 static gboolean
-_cogl_pipeline_alpha_state_equal (CoglPipeline *authority0,
-                                  CoglPipeline *authority1)
+_cogl_pipeline_alpha_func_state_equal (CoglPipeline *authority0,
+                                       CoglPipeline *authority1)
 {
   CoglPipelineAlphaFuncState *alpha_state0 =
     &authority0->big_state->alpha_state;
   CoglPipelineAlphaFuncState *alpha_state1 =
     &authority1->big_state->alpha_state;
 
-  if (alpha_state0->alpha_func != alpha_state1->alpha_func ||
-      alpha_state0->alpha_func_reference != alpha_state1->alpha_func_reference)
-    return FALSE;
-  else
-    return TRUE;
+  return alpha_state0->alpha_func == alpha_state1->alpha_func;
+}
+
+static gboolean
+_cogl_pipeline_alpha_func_reference_state_equal (CoglPipeline *authority0,
+                                                 CoglPipeline *authority1)
+{
+  CoglPipelineAlphaFuncState *alpha_state0 =
+    &authority0->big_state->alpha_state;
+  CoglPipelineAlphaFuncState *alpha_state1 =
+    &authority1->big_state->alpha_state;
+
+  return (alpha_state0->alpha_func_reference ==
+          alpha_state1->alpha_func_reference);
 }
 
 static gboolean
@@ -3315,7 +3325,13 @@ _cogl_pipeline_equal (CoglPipeline *pipeline0,
   if (!simple_property_equal (pipeline0, pipeline1,
                               pipelines_difference,
                               COGL_PIPELINE_STATE_ALPHA_FUNC,
-                              _cogl_pipeline_alpha_state_equal))
+                              _cogl_pipeline_alpha_func_state_equal))
+    goto done;
+
+  if (!simple_property_equal (pipeline0, pipeline1,
+                              pipelines_difference,
+                              COGL_PIPELINE_STATE_ALPHA_FUNC_REFERENCE,
+                              _cogl_pipeline_alpha_func_reference_state_equal))
     goto done;
 
   /* We don't need to compare the detailed blending state if we know
@@ -3834,10 +3850,9 @@ cogl_pipeline_set_emission (CoglPipeline *pipeline, const CoglColor *emission)
   handle_automatic_blend_enable (pipeline, state);
 }
 
-void
-cogl_pipeline_set_alpha_test_function (CoglPipeline *pipeline,
-				       CoglPipelineAlphaFunc alpha_func,
-				       float alpha_reference)
+static void
+_cogl_pipeline_set_alpha_test_function (CoglPipeline *pipeline,
+                                        CoglPipelineAlphaFunc alpha_func)
 {
   CoglPipelineState state = COGL_PIPELINE_STATE_ALPHA_FUNC;
   CoglPipeline *authority;
@@ -3848,8 +3863,7 @@ cogl_pipeline_set_alpha_test_function (CoglPipeline *pipeline,
   authority = _cogl_pipeline_get_authority (pipeline, state);
 
   alpha_state = &authority->big_state->alpha_state;
-  if (alpha_state->alpha_func == alpha_func &&
-      alpha_state->alpha_func_reference == alpha_reference)
+  if (alpha_state->alpha_func == alpha_func)
     return;
 
   /* - Flush journal primitives referencing the current state.
@@ -3861,10 +3875,51 @@ cogl_pipeline_set_alpha_test_function (CoglPipeline *pipeline,
 
   alpha_state = &pipeline->big_state->alpha_state;
   alpha_state->alpha_func = alpha_func;
-  alpha_state->alpha_func_reference = alpha_reference;
 
   _cogl_pipeline_update_authority (pipeline, authority, state,
-                                   _cogl_pipeline_alpha_state_equal);
+                                   _cogl_pipeline_alpha_func_state_equal);
+}
+
+static void
+_cogl_pipeline_set_alpha_test_function_reference (CoglPipeline *pipeline,
+                                                  float alpha_reference)
+{
+  CoglPipelineState state = COGL_PIPELINE_STATE_ALPHA_FUNC_REFERENCE;
+  CoglPipeline *authority;
+  CoglPipelineAlphaFuncState *alpha_state;
+
+  g_return_if_fail (cogl_is_pipeline (pipeline));
+
+  authority = _cogl_pipeline_get_authority (pipeline, state);
+
+  alpha_state = &authority->big_state->alpha_state;
+  if (alpha_state->alpha_func_reference == alpha_reference)
+    return;
+
+  /* - Flush journal primitives referencing the current state.
+   * - Make sure the pipeline has no dependants so it may be modified.
+   * - If the pipeline isn't currently an authority for the state being
+   *   changed, then initialize that state from the current authority.
+   */
+  _cogl_pipeline_pre_change_notify (pipeline, state, NULL, FALSE);
+
+  alpha_state = &pipeline->big_state->alpha_state;
+  alpha_state->alpha_func_reference = alpha_reference;
+
+  _cogl_pipeline_update_authority
+    (pipeline, authority, state,
+     _cogl_pipeline_alpha_func_reference_state_equal);
+}
+
+void
+cogl_pipeline_set_alpha_test_function (CoglPipeline *pipeline,
+				       CoglPipelineAlphaFunc alpha_func,
+				       float alpha_reference)
+{
+  _cogl_pipeline_set_alpha_test_function (pipeline, alpha_func);
+  _cogl_pipeline_set_alpha_test_function_reference (pipeline, alpha_reference);
+}
+
 }
 
 GLenum
@@ -5743,6 +5798,13 @@ _cogl_pipeline_find_codegen_authority (CoglPipeline *pipeline,
   int n_layers;
   CoglPipelineLayer **authority0_layers;
   CoglPipelineLayer **authority1_layers;
+  /* Under GLES2 the alpha func becomes part of the fragment program
+     so we can't share programs there */
+  const int codegen_state = (COGL_PIPELINE_STATE_LAYERS
+#ifdef HAVE_COGL_GLES2
+                             | COGL_PIPELINE_STATE_ALPHA_FUNC
+#endif
+                             );
 
   /* XXX: we'll need to update this when we add fog support to the
    * codegen */
@@ -5753,7 +5815,7 @@ _cogl_pipeline_find_codegen_authority (CoglPipeline *pipeline,
   /* Find the first pipeline that modifies state that affects the
    * codegen... */
   authority0 = _cogl_pipeline_get_authority (pipeline,
-                                             COGL_PIPELINE_STATE_LAYERS);
+                                             codegen_state);
 
   /* Find the next ancestor after that, that also modifies state
    * affecting codegen... */
@@ -5761,7 +5823,7 @@ _cogl_pipeline_find_codegen_authority (CoglPipeline *pipeline,
     {
       authority1 =
         _cogl_pipeline_get_authority (_cogl_pipeline_get_parent (authority0),
-                                      COGL_PIPELINE_STATE_LAYERS);
+                                      codegen_state);
     }
   else
     return authority0;
@@ -5804,7 +5866,7 @@ _cogl_pipeline_find_codegen_authority (CoglPipeline *pipeline,
       authority0 = authority1;
       authority1 =
         _cogl_pipeline_get_authority (_cogl_pipeline_get_parent (authority1),
-                                      COGL_PIPELINE_STATE_LAYERS);
+                                      codegen_state);
       if (authority1 == authority0)
         break;
     }