diff --git a/Source/Core/VideoCommon/Src/BPStructs.cpp b/Source/Core/VideoCommon/Src/BPStructs.cpp
index 7773773439..e0b0c9bca2 100644
--- a/Source/Core/VideoCommon/Src/BPStructs.cpp
+++ b/Source/Core/VideoCommon/Src/BPStructs.cpp
@@ -358,7 +358,7 @@ void BPWritten(const Bypass& bp)
 #endif
 		break;
 						   }
-	case BPMEM_ZCOMPARE:      // Set the Z-Compare
+	case BPMEM_ZCOMPARE:      // Set the Z-Compare and EFB pixel format
 	case BPMEM_TEXINVALIDATE: // Used, if game has manual control the Texture Cache, which we don't allow
 	case BPMEM_MIPMAP_STRIDE: // MipMap Stride Channel
 	case BPMEM_COPYYSCALE:    // Display Copy Y Scale
diff --git a/Source/Plugins/Plugin_VideoOGL/Src/BPFunctions.cpp b/Source/Plugins/Plugin_VideoOGL/Src/BPFunctions.cpp
index 3c5992f0b1..51f4121954 100644
--- a/Source/Plugins/Plugin_VideoOGL/Src/BPFunctions.cpp
+++ b/Source/Plugins/Plugin_VideoOGL/Src/BPFunctions.cpp
@@ -156,10 +156,15 @@ void ClearScreen(const Bypass &bp, const TRectangle &multirc)
         if (bpmem.blendmode.colorupdate || bpmem.blendmode.alphaupdate)
 		{
             u32 clearColor = (bpmem.clearcolorAR << 16) | bpmem.clearcolorGB;
+
+			// Alpha may or may not be present depending on the EFB pixel format.
+			GLclampf clearAlpha = (bpmem.zcontrol.pixel_format == PIXELFMT_RGBA6_Z24) ?
+				((clearColor>>24) & 0xff)*(1/255.0f) : 1.0f;
+
 			glClearColor(((clearColor>>16) & 0xff)*(1/255.0f),
 						 ((clearColor>>8 ) & 0xff)*(1/255.0f),
 						 ((clearColor>>0 ) & 0xff)*(1/255.0f),
-						 ((clearColor>>24) & 0xff)*(1/255.0f));
+						 clearAlpha);
             bits |= GL_COLOR_BUFFER_BIT;
         }
         if (bpmem.zmode.updateenable)
diff --git a/Source/Plugins/Plugin_VideoOGL/Src/FramebufferManager.cpp b/Source/Plugins/Plugin_VideoOGL/Src/FramebufferManager.cpp
index 49f804b91a..1c531db68d 100644
--- a/Source/Plugins/Plugin_VideoOGL/Src/FramebufferManager.cpp
+++ b/Source/Plugins/Plugin_VideoOGL/Src/FramebufferManager.cpp
@@ -25,6 +25,17 @@ void FramebufferManager::Init(int targetWidth, int targetHeight, int msaaSamples
 	m_msaaSamples = msaaSamples;
 	m_msaaCoverageSamples = msaaCoverageSamples;
 
+	// The EFB can be set to different pixel formats by the game through the
+	// BPMEM_ZCOMPARE register (which should probably have a different name).
+	// They are:
+	// - 24-bit RGB (8-bit components) with 24-bit Z
+	// - 24-bit RGBA (6-bit components) with 24-bit Z
+	// - Multisampled 16-bit RGB (5-6-5 format) with 16-bit Z
+	// We only use one EFB format here: 32-bit ARGB with 24-bit Z.
+	// Multisampling depends on user settings.
+	// The distinction becomes important for certain operations, i.e. the
+	// alpha channel should be ignored if the EFB does not have one.
+
 	// Create EFB target.
 
 	glGenFramebuffersEXT(1, &m_efbFramebuffer);