diff --git a/arch/arm/imx-common/cpu.c b/arch/arm/imx-common/cpu.c
index 40fe813d29..74bdd24ed1 100644
--- a/arch/arm/imx-common/cpu.c
+++ b/arch/arm/imx-common/cpu.c
@@ -275,6 +275,9 @@ u32 get_ahb_clk(void)
 
 void arch_preboot_os(void)
 {
+#if defined(CONFIG_PCIE_IMX)
+	imx_pcie_remove();
+#endif
 #if defined(CONFIG_CMD_SATA)
 	sata_stop();
 #if defined(CONFIG_MX6)
diff --git a/drivers/pci/pcie_imx.c b/drivers/pci/pcie_imx.c
index 732d59d711..eab0a2b602 100644
--- a/drivers/pci/pcie_imx.c
+++ b/drivers/pci/pcie_imx.c
@@ -42,6 +42,9 @@
 
 /* PCIe Port Logic registers (memory-mapped) */
 #define PL_OFFSET 0x700
+#define PCIE_PL_PFLR (PL_OFFSET + 0x08)
+#define PCIE_PL_PFLR_LINK_STATE_MASK		(0x3f << 16)
+#define PCIE_PL_PFLR_FORCE_LINK			(1 << 15)
 #define PCIE_PHY_DEBUG_R0 (PL_OFFSET + 0x28)
 #define PCIE_PHY_DEBUG_R1 (PL_OFFSET + 0x2c)
 #define PCIE_PHY_DEBUG_R1_LINK_UP		(1 << 4)
@@ -445,6 +448,36 @@ static int imx6_pcie_assert_core_reset(void)
 	/* Power up PCIe PHY */
 	setbits_le32(&gpc_regs->cntr, PCIE_PHY_PUP_REQ);
 #else
+	/*
+	 * If the bootloader already enabled the link we need some special
+	 * handling to get the core back into a state where it is safe to
+	 * touch it for configuration.  As there is no dedicated reset signal
+	 * wired up for MX6QDL, we need to manually force LTSSM into "detect"
+	 * state before completely disabling LTSSM, which is a prerequisite
+	 * for core configuration.
+	 *
+	 * If both LTSSM_ENABLE and REF_SSP_ENABLE are active we have a strong
+	 * indication that the bootloader activated the link.
+	 */
+	if (is_mx6dq()) {
+		u32 val, gpr1, gpr12;
+
+		gpr1 = readl(&iomuxc_regs->gpr[1]);
+		gpr12 = readl(&iomuxc_regs->gpr[12]);
+		if ((gpr1 & IOMUXC_GPR1_PCIE_REF_CLK_EN) &&
+		    (gpr12 & IOMUXC_GPR12_PCIE_CTL_2)) {
+			val = readl(MX6_DBI_ADDR + PCIE_PL_PFLR);
+			val &= ~PCIE_PL_PFLR_LINK_STATE_MASK;
+			val |= PCIE_PL_PFLR_FORCE_LINK;
+
+			imx_pcie_fix_dabt_handler(true);
+			writel(val, MX6_DBI_ADDR + PCIE_PL_PFLR);
+			imx_pcie_fix_dabt_handler(false);
+
+			gpr12 &= ~IOMUXC_GPR12_PCIE_CTL_2;
+			writel(val, &iomuxc_regs->gpr[12]);
+		}
+	}
 	setbits_le32(&iomuxc_regs->gpr[1], IOMUXC_GPR1_TEST_POWERDOWN);
 	clrbits_le32(&iomuxc_regs->gpr[1], IOMUXC_GPR1_REF_SSP_EN);
 #endif
@@ -652,6 +685,11 @@ void imx_pcie_init(void)
 	}
 }
 
+void imx_pcie_remove(void)
+{
+	imx6_pcie_assert_core_reset();
+}
+
 /* Probe function. */
 void pci_init_board(void)
 {
diff --git a/include/pci.h b/include/pci.h
index d3c955eb80..c8ef997d0d 100644
--- a/include/pci.h
+++ b/include/pci.h
@@ -754,6 +754,10 @@ int pci_last_busno(void);
 extern void pci_mpc85xx_init (struct pci_controller *hose);
 #endif
 
+#ifdef CONFIG_PCIE_IMX
+extern void imx_pcie_remove(void);
+#endif
+
 #if !defined(CONFIG_DM_PCI) || defined(CONFIG_DM_PCI_COMPAT)
 /**
  * pci_write_bar32() - Write the address of a BAR including control bits