diff --git a/src/mainboard/pcengines/apu1/mainboard.c b/src/mainboard/pcengines/apu1/mainboard.c
index f80f24ec87..82cf9921a5 100644
--- a/src/mainboard/pcengines/apu1/mainboard.c
+++ b/src/mainboard/pcengines/apu1/mainboard.c
@@ -183,6 +183,18 @@ static void mainboard_enable(device_t dev)
 
 	config_gpio_mux();
 
+	/* Power off unused clock pins of GPP PCIe devices */
+	u8 *misc_mem_clk_cntrl = (u8 *)(ACPI_MMIO_BASE + MISC_BASE);
+	/* GPP CLK0-2 are connected to the 3 ethernet chips
+	 * GPP CLK3-4 are connected to the miniPCIe slots */
+	write8(misc_mem_clk_cntrl + 0, 0xFF);
+	write8(misc_mem_clk_cntrl + 1, 0xFF);
+	/* GPP CLK5 is only connected to test pads -> disable */
+	write8(misc_mem_clk_cntrl + 2, 0x0F);
+	/* disable unconnected GPP CLK6-8 and SLT_GFX_CLK */
+	write8(misc_mem_clk_cntrl + 3, 0x00);
+	write8(misc_mem_clk_cntrl + 4, 0x00);
+
 	/* Initialize the PIRQ data structures for consumption */
 	pirq_setup();
 }
diff --git a/src/mainboard/pcengines/apu1/platform_cfg.h b/src/mainboard/pcengines/apu1/platform_cfg.h
index 946f238bdd..7172e8283e 100644
--- a/src/mainboard/pcengines/apu1/platform_cfg.h
+++ b/src/mainboard/pcengines/apu1/platform_cfg.h
@@ -69,12 +69,12 @@
  *   0 - disable
  *   1 - enable
  *  PCI SLOT 0 define at BIT0
- *  PCI SLOT 1 define at BIT1
+ *  PCI SLOT 1 define at BIT1 -> connected to LPC devices
  *  PCI SLOT 2 define at BIT2
  *  PCI SLOT 3 define at BIT3
  *  PCI SLOT 4 define at BIT4
  */
-#define PCI_CLOCK_CTRL			0x1F
+#define PCI_CLOCK_CTRL			0x02
 
 /**
  * @def SATA_CONTROLLER