diff --git a/Source/Core/VideoCommon/GXPipelineTypes.h b/Source/Core/VideoCommon/GXPipelineTypes.h
index 8892d386f5..694c368ef6 100644
--- a/Source/Core/VideoCommon/GXPipelineTypes.h
+++ b/Source/Core/VideoCommon/GXPipelineTypes.h
@@ -20,8 +20,7 @@ namespace VideoCommon
 // As pipelines encompass both shader UIDs and render states, changes to either of these should
 // also increment the pipeline UID version. Incrementing the UID version will cause all UID
 // caches to be invalidated.
-// TODO: Remove PixelShaderUid hasindstage on the next UID version bump
-constexpr u32 GX_PIPELINE_UID_VERSION = 2;  // Last changed in PR 9122
+constexpr u32 GX_PIPELINE_UID_VERSION = 3;  // Last changed in PR 9532
 
 struct GXPipelineUid
 {
diff --git a/Source/Core/VideoCommon/PixelShaderGen.cpp b/Source/Core/VideoCommon/PixelShaderGen.cpp
index 37e856ae42..567d161565 100644
--- a/Source/Core/VideoCommon/PixelShaderGen.cpp
+++ b/Source/Core/VideoCommon/PixelShaderGen.cpp
@@ -236,12 +236,6 @@ PixelShaderUid GetPixelShaderUid()
   for (unsigned int n = 0; n < numStages; n++)
   {
     uid_data->stagehash[n].tevorders_texcoord = bpmem.tevorders[n / 2].getTexCoord(n & 1);
-
-    // hasindstage previously was used as a criterion to set tevind to 0, but there are variables in
-    // tevind that are used even if the indirect stage is disabled, so now it is only left in to
-    // avoid breaking existing UIDs (in most cases, games will have 0 in tevind anyways)
-    // TODO: Remove hasindstage on the next UID version bump
-    uid_data->stagehash[n].hasindstage = bpmem.tevind[n].bt < bpmem.genMode.numindstages;
     uid_data->stagehash[n].tevind = bpmem.tevind[n].hex;
 
     TevStageCombiner::ColorCombiner& cc = bpmem.combiners[n].colorC;
diff --git a/Source/Core/VideoCommon/PixelShaderGen.h b/Source/Core/VideoCommon/PixelShaderGen.h
index d75fac8eb7..b1f2c20681 100644
--- a/Source/Core/VideoCommon/PixelShaderGen.h
+++ b/Source/Core/VideoCommon/PixelShaderGen.h
@@ -130,11 +130,9 @@ struct pixel_shader_uid_data
     u32 tevorders_texcoord : 3;
     u32 tevorders_enable : 1;
     RasColorChan tevorders_colorchan : 3;
-    u32 pad1 : 6;
+    u32 pad1 : 7;
 
     // TODO: Clean up the swapXY mess
-    // TODO: remove hasindstage, as it no longer does anything useful
-    u32 hasindstage : 1;
     u32 tevind : 21;
     u32 tevksel_swap1a : 2;
     u32 tevksel_swap2a : 2;