diff --git a/GPU/Common/ShaderId.cpp b/GPU/Common/ShaderId.cpp
index 46fc89e8aa..d7da61c290 100644
--- a/GPU/Common/ShaderId.cpp
+++ b/GPU/Common/ShaderId.cpp
@@ -91,7 +91,6 @@ void ComputeVertexShaderID(VShaderID *id_out, VertexDecoder *vertexDecoder, bool
 		!isModeThrough && gstate_c.submitType == SubmitType::DRAW;  // neither hw nor sw spline/bezier. See #11692
 
 	VShaderID id;
-	id.SetBit(VS_BIT_LMODE, lmode);
 	id.SetBit(VS_BIT_IS_THROUGH, isModeThrough);
 	id.SetBit(VS_BIT_HAS_COLOR, vtypeHasColor);
 	id.SetBit(VS_BIT_VERTEX_RANGE_CULLING, vertexRangeCulling);
@@ -134,6 +133,7 @@ void ComputeVertexShaderID(VShaderID *id_out, VertexDecoder *vertexDecoder, bool
 			// doShadeMapping is stored as UVGenMode, and light type doesn't matter for shade mapping.
 			id.SetBit(VS_BIT_LIGHTING_ENABLE);
 			if (gstate_c.Use(GPU_USE_LIGHT_UBERSHADER)) {
+				lmode = false;  // handled dynamically.
 				id.SetBit(VS_BIT_LIGHT_UBERSHADER);
 			} else {
 				id.SetBits(VS_BIT_MATERIAL_UPDATE, 3, gstate.getMaterialUpdate());
@@ -165,6 +165,7 @@ void ComputeVertexShaderID(VShaderID *id_out, VertexDecoder *vertexDecoder, bool
 		}
 	}
 
+	id.SetBit(VS_BIT_LMODE, lmode);
 	id.SetBit(VS_BIT_FLATSHADE, doFlatShading);
 
 	// These two bits cannot be combined, otherwise havoc occurs. We get reports that indicate this happened somehow... "ERROR: 0:14: 'u_proj' : undeclared identifier"
diff --git a/GPU/Common/ShaderUniforms.cpp b/GPU/Common/ShaderUniforms.cpp
index 17229c540e..92c22be0fe 100644
--- a/GPU/Common/ShaderUniforms.cpp
+++ b/GPU/Common/ShaderUniforms.cpp
@@ -274,6 +274,7 @@ void BaseUpdateUniforms(UB_VS_FS_Base *ub, uint64_t dirtyUniforms, bool flipView
 	}
 }
 
+// For "light ubershader" bits.
 uint32_t PackLightControlBits() {
 	// Bit organization
 	// Bottom 4 bits are enable bits for each light.
@@ -292,8 +293,10 @@ uint32_t PackLightControlBits() {
 		lightControl |= type << (4 + i * 4 + 2);
 	}
 
+	// Material update is 3 bits.
 	lightControl |= gstate.getMaterialUpdate() << 20;
-
+	// LMODE is 1 bit.
+	lightControl |= gstate.isUsingSecondaryColor() << 23;
 	return lightControl;
 }
 
diff --git a/GPU/Common/VertexShaderGenerator.cpp b/GPU/Common/VertexShaderGenerator.cpp
index 966ee93ece..295de3ab21 100644
--- a/GPU/Common/VertexShaderGenerator.cpp
+++ b/GPU/Common/VertexShaderGenerator.cpp
@@ -1157,13 +1157,24 @@ bool GenerateVertexShader(const VShaderID &id, char *buffer, const ShaderLanguag
 				WRITE(p, "  %sv_color0 = lightSum0;\n", compat.vsOutPrefix);
 				WRITE(p, "  %sv_color1 = splat3(0.0);\n", compat.vsOutPrefix);
 			} else {
-				if (lmode) {
-					WRITE(p, "  %sv_color0 = lightSum0;\n", compat.vsOutPrefix);
-					// v_color1 only exists when lmode = 1.
-					WRITE(p, "  %sv_color1 = clamp(lightSum1, 0.0, 1.0);\n", compat.vsOutPrefix);
+				if (lightUberShader) {
+					p.C("  bool lmode = (u_lightControl & (0x1u << 0x17u)) != 0u;\n");
+					p.C("  if (lmode) {");
+					p.F("    %sv_color0 = lightSum0;\n", compat.vsOutPrefix);
+					p.F("    %sv_color1 = clamp(lightSum1, 0.0, 1.0);\n", compat.vsOutPrefix);
+					p.C("  } else {");
+					p.F("    %sv_color0 = clamp(lightSum0 + vec4(lightSum1, 0.0), 0.0, 1.0);\n", compat.vsOutPrefix);
+					p.F("    %sv_color1 = splat3(0.0);\n", compat.vsOutPrefix);
+					p.C("  }");
 				} else {
-					WRITE(p, "  %sv_color0 = clamp(lightSum0 + vec4(lightSum1, 0.0), 0.0, 1.0);\n", compat.vsOutPrefix);
-					WRITE(p, "  %sv_color1 = splat3(0.0);\n", compat.vsOutPrefix);
+					if (lmode) {
+						WRITE(p, "  %sv_color0 = lightSum0;\n", compat.vsOutPrefix);
+						// v_color1 only exists when lmode = 1.
+						WRITE(p, "  %sv_color1 = clamp(lightSum1, 0.0, 1.0);\n", compat.vsOutPrefix);
+					} else {
+						WRITE(p, "  %sv_color0 = clamp(lightSum0 + vec4(lightSum1, 0.0), 0.0, 1.0);\n", compat.vsOutPrefix);
+						WRITE(p, "  %sv_color1 = splat3(0.0);\n", compat.vsOutPrefix);
+					}
 				}
 			}
 		} else {
diff --git a/GPU/GPUCommon.cpp b/GPU/GPUCommon.cpp
index a9c4b9318c..8cc6004347 100644
--- a/GPU/GPUCommon.cpp
+++ b/GPU/GPUCommon.cpp
@@ -113,8 +113,8 @@ const CommonCommandTableEntry commonCommandTable[] = {
 	{ GE_CMD_LIGHTTYPE3, FLAG_FLUSHBEFOREONCHANGE, DIRTY_VERTEXSHADER_STATE | DIRTY_LIGHT3 },
 	{ GE_CMD_MATERIALUPDATE, FLAG_FLUSHBEFOREONCHANGE, DIRTY_VERTEXSHADER_STATE },
 
-	// These change both shaders so need flushing.
-	{ GE_CMD_LIGHTMODE, FLAG_FLUSHBEFOREONCHANGE, DIRTY_VERTEXSHADER_STATE | DIRTY_FRAGMENTSHADER_STATE | DIRTY_GEOMETRYSHADER_STATE },
+	// These change vertex shaders (in non uber shader mode) so need flushing.
+	{ GE_CMD_LIGHTMODE, FLAG_FLUSHBEFOREONCHANGE, DIRTY_VERTEXSHADER_STATE },
 
 	{ GE_CMD_TEXFILTER, FLAG_FLUSHBEFOREONCHANGE, DIRTY_TEXTURE_PARAMS },
 	{ GE_CMD_TEXWRAP, FLAG_FLUSHBEFOREONCHANGE, DIRTY_TEXTURE_PARAMS | DIRTY_FRAGMENTSHADER_STATE },
@@ -472,9 +472,11 @@ void GPUCommon::UpdateCmdInfo() {
 	if (gstate_c.Use(GPU_USE_LIGHT_UBERSHADER)) {
 		cmdInfo_[GE_CMD_MATERIALUPDATE].RemoveDirty(DIRTY_VERTEXSHADER_STATE);
 		cmdInfo_[GE_CMD_MATERIALUPDATE].AddDirty(DIRTY_LIGHT_CONTROL);
+		cmdInfo_[GE_CMD_LIGHTMODE].AddDirty(DIRTY_LIGHT_CONTROL);
 	} else {
 		cmdInfo_[GE_CMD_MATERIALUPDATE].RemoveDirty(DIRTY_LIGHT_CONTROL);
 		cmdInfo_[GE_CMD_MATERIALUPDATE].AddDirty(DIRTY_VERTEXSHADER_STATE);
+		cmdInfo_[GE_CMD_LIGHTMODE].RemoveDirty(DIRTY_LIGHT_CONTROL);
 	}
 }