diff --git a/pcsx2/Linux/LnxMain.cpp b/pcsx2/Linux/LnxMain.cpp
index 219864c43f..d61d69676a 100644
--- a/pcsx2/Linux/LnxMain.cpp
+++ b/pcsx2/Linux/LnxMain.cpp
@@ -17,7 +17,6 @@
  */
 
 #include "LnxMain.h"
-#include "CDVD/CDVDisoReader.h"
 
 using namespace R5900;
 
diff --git a/pcsx2/Linux/LnxMain.h b/pcsx2/Linux/LnxMain.h
index 86b74cebd0..7639f9f7b6 100644
--- a/pcsx2/Linux/LnxMain.h
+++ b/pcsx2/Linux/LnxMain.h
@@ -23,6 +23,9 @@
 #include "LnxMain.h"
 #include "HostGui.h"
 
+// For Linux ISO loading
+#include "CDVD/CDVDisoReader.h"
+
 extern bool applychanges;
 extern bool Slots[5];
 
diff --git a/pcsx2/Linux/LnxSysExec.cpp b/pcsx2/Linux/LnxSysExec.cpp
index e5da6434f0..2bd55604c5 100644
--- a/pcsx2/Linux/LnxSysExec.cpp
+++ b/pcsx2/Linux/LnxSysExec.cpp
@@ -183,16 +183,26 @@ void RunGui()
 	{
 		// Initially bypass GUI and start PCSX2 directly.
 		// Manually load plugins using the user's configured image (if non-elf).
+
+		int mode = g_Startup.BootMode & BootMode_ModeMask;
 		
-		if( g_Startup.Enabled && (g_Startup.BootMode != BootMode_Elf) )
+		if( g_Startup.Enabled && (mode != BootMode_Elf) )
 		{
+
+			if(mode == BootMode_Iso)
+				CDVD = ISO;
+			else if(mode == BootMode_NoDisc)
+				CDVD = NODISC;
+			else
+				CDVD = CDVD_plugin;
+
 			if (OpenPlugins(g_Startup.ImageName) == -1)
 				return;
 		}
 
 		SysPrepareExecution(
 			(g_Startup.BootMode == BootMode_Elf) ? g_Startup.ImageName : NULL, 
-			(g_Startup.BootMode == BootMode_Bios)
+			((g_Startup.BootMode & BootMode_Bios) != 0)
 		);
 	}
 	
diff --git a/pcsx2/Linux/LnxSysExec.h b/pcsx2/Linux/LnxSysExec.h
index 639a7e7671..b429712848 100644
--- a/pcsx2/Linux/LnxSysExec.h
+++ b/pcsx2/Linux/LnxSysExec.h
@@ -24,6 +24,9 @@
 #include <sys/mman.h>
 #include "x86/iR5900.h"
 
+// For Linux ISO loading
+#include "CDVD/CDVDisoReader.h"
+
 void SysPageFaultExceptionFilter( int signal, siginfo_t *info, void * );
 void __fastcall InstallLinuxExceptionHandler();
 void __fastcall ReleaseLinuxExceptionHandler();