diff --git a/.cproject b/.cproject
index f01bbf6..2db39f7 100644
--- a/.cproject
+++ b/.cproject
@@ -38,7 +38,7 @@
 									<listOptionValue builtIn="false" value="FIXED_CONTROL_ENDPOINT_SIZE=8"/>
 									<listOptionValue builtIn="false" value="FIXED_NUM_CONFIGURATIONS=1"/>
 									<listOptionValue builtIn="false" value="USE_FLASH_DESCRIPTORS"/>
-									<listOptionValue builtIn="false" value="USE_STATIC_OPTIONS=&quot;(USB_DEVICE_OPT_FULLSPEED | USB_OPT_REG_ENABLED | USB_OPT_AUTO_PLL)&quot;"/>
+									<listOptionValue builtIn="false" value="USE_STATIC_OPTIONS=&quot;(USB_DEVICE_OPT_FULLSPEED | USB_OPT_REG_ENABLED | USB_OPT_MANUAL_PLL)&quot;"/>
 								</option>
 								<option id="de.innot.avreclipse.compiler.option.otherflags.1513967861" name="Other flags" superClass="de.innot.avreclipse.compiler.option.otherflags" value="-ffunction-sections -fdata-sections" valueType="string"/>
 								<option IS_BUILTIN_EMPTY="false" IS_VALUE_EMPTY="false" id="de.innot.avreclipse.compiler.option.incpath.173462079" superClass="de.innot.avreclipse.compiler.option.incpath" valueType="includePath">
@@ -113,7 +113,7 @@
 									<listOptionValue builtIn="false" value="FIXED_CONTROL_ENDPOINT_SIZE=8"/>
 									<listOptionValue builtIn="false" value="FIXED_NUM_CONFIGURATIONS=1"/>
 									<listOptionValue builtIn="false" value="USE_FLASH_DESCRIPTORS"/>
-									<listOptionValue builtIn="false" value="USE_STATIC_OPTIONS=&quot;(USB_DEVICE_OPT_FULLSPEED | USB_OPT_REG_ENABLED | USB_OPT_AUTO_PLL)&quot;"/>
+									<listOptionValue builtIn="false" value="USE_STATIC_OPTIONS=&quot;(USB_DEVICE_OPT_FULLSPEED | USB_OPT_REG_ENABLED | USB_OPT_MANUAL_PLL)&quot;"/>
 								</option>
 								<option id="de.innot.avreclipse.compiler.option.otherflags.1566165436" name="Other flags" superClass="de.innot.avreclipse.compiler.option.otherflags" value="-ffunction-sections -fdata-sections" valueType="string"/>
 								<option IS_BUILTIN_EMPTY="false" IS_VALUE_EMPTY="false" id="de.innot.avreclipse.compiler.option.incpath.2119807530" superClass="de.innot.avreclipse.compiler.option.incpath" valueType="includePath">
diff --git a/hal/at90usb646/usbcdc.c b/hal/at90usb646/usbcdc.c
index baf84d5..6f3cf8a 100644
--- a/hal/at90usb646/usbcdc.c
+++ b/hal/at90usb646/usbcdc.c
@@ -25,13 +25,29 @@
 #include "../usbcdc.h"
 #include "LUFA/Drivers/USB/USB.h"
 #include "cdc_device_definition.h"
+#include "hardware.h"
 
 /** Initializes the USB CDC device
  *
  */
 void USBCDC_Init(void)
 {
-	// Initialize LUFA
+	// Initialize LUFA.
+	// We have to manually start the USB PLL rather than allow LUFA to do it,
+	// because we might be on an AT90USB128x instead of AT90USB64x, and LUFA's
+	// automatic PLL control decides on the PLL init value at compile time.
+	// It differs between the two chips when there's a 16 MHz crystal.
+	if (IsAT90USB128x())
+	{
+		PLLCSR = (1 << PLLP2) | (1 << PLLP0);
+		PLLCSR = ((1 << PLLP2) | (1 << PLLP0) | (1 << PLLE));
+	}
+	else
+	{
+		PLLCSR = (1 << PLLP2) | (1 << PLLP1);
+		PLLCSR = ((1 << PLLP2) | (1 << PLLP1) | (1 << PLLE));
+	}
+	while (!USB_PLL_IsReady());
 	USB_Init();
 }
 
@@ -42,6 +58,7 @@ void USBCDC_Disable(void)
 {
 	// Disable LUFA, this will cause us to no longer identify as a USB device
 	USB_Disable();
+	USB_PLL_Off();
 }
 
 /** Main loop handler for the USB CDC device. Call from the main loop.