diff --git a/drivers/pci/host/pci-imx6.c b/drivers/pci/host/pci-imx6.c
index d81da4556c19b8bfa51a2b05d03f6d9f11c34a4c..d34678dc5a14a80263bac47b44bfd6e848570cc6 100644
--- a/drivers/pci/host/pci-imx6.c
+++ b/drivers/pci/host/pci-imx6.c
@@ -44,6 +44,12 @@ struct imx6_pcie {
 	void __iomem		*mem_base;
 };
 
+/* PCIe Root Complex registers (memory-mapped) */
+#define PCIE_RC_LCR				0x7c
+#define PCIE_RC_LCR_MAX_LINK_SPEEDS_GEN1	0x1
+#define PCIE_RC_LCR_MAX_LINK_SPEEDS_GEN2	0x2
+#define PCIE_RC_LCR_MAX_LINK_SPEEDS_MASK	0xf
+
 /* PCIe Port Logic registers (memory-mapped) */
 #define PL_OFFSET 0x700
 #define PCIE_PHY_DEBUG_R0 (PL_OFFSET + 0x28)
@@ -61,6 +67,9 @@ struct imx6_pcie {
 #define PCIE_PHY_STAT (PL_OFFSET + 0x110)
 #define PCIE_PHY_STAT_ACK_LOC 16
 
+#define PCIE_LINK_WIDTH_SPEED_CONTROL	0x80C
+#define PORT_LOGIC_SPEED_CHANGE		(0x1 << 17)
+
 /* PHY registers (not memory-mapped) */
 #define PCIE_PHY_RX_ASIC_OUT 0x100D
 
@@ -323,11 +332,71 @@ static int imx6_pcie_wait_for_link(struct pcie_port *pp)
 	return 0;
 }
 
-static void imx6_pcie_host_init(struct pcie_port *pp)
+static int imx6_pcie_start_link(struct pcie_port *pp)
 {
-	int count = 0;
 	struct imx6_pcie *imx6_pcie = to_imx6_pcie(pp);
+	uint32_t tmp;
+	int ret, count;
+
+	/*
+	 * Force Gen1 operation when starting the link.  In case the link is
+	 * started in Gen2 mode, there is a possibility the devices on the
+	 * bus will not be detected at all.  This happens with PCIe switches.
+	 */
+	tmp = readl(pp->dbi_base + PCIE_RC_LCR);
+	tmp &= ~PCIE_RC_LCR_MAX_LINK_SPEEDS_MASK;
+	tmp |= PCIE_RC_LCR_MAX_LINK_SPEEDS_GEN1;
+	writel(tmp, pp->dbi_base + PCIE_RC_LCR);
+
+	/* Start LTSSM. */
+	regmap_update_bits(imx6_pcie->iomuxc_gpr, IOMUXC_GPR12,
+			IMX6Q_GPR12_PCIE_CTL_2, 1 << 10);
+
+	ret = imx6_pcie_wait_for_link(pp);
+	if (ret)
+		return ret;
+
+	/* Allow Gen2 mode after the link is up. */
+	tmp = readl(pp->dbi_base + PCIE_RC_LCR);
+	tmp &= ~PCIE_RC_LCR_MAX_LINK_SPEEDS_MASK;
+	tmp |= PCIE_RC_LCR_MAX_LINK_SPEEDS_GEN2;
+	writel(tmp, pp->dbi_base + PCIE_RC_LCR);
+
+	/*
+	 * Start Directed Speed Change so the best possible speed both link
+	 * partners support can be negotiated.
+	 */
+	tmp = readl(pp->dbi_base + PCIE_LINK_WIDTH_SPEED_CONTROL);
+	tmp |= PORT_LOGIC_SPEED_CHANGE;
+	writel(tmp, pp->dbi_base + PCIE_LINK_WIDTH_SPEED_CONTROL);
+
+	count = 200;
+	while (count--) {
+		tmp = readl(pp->dbi_base + PCIE_LINK_WIDTH_SPEED_CONTROL);
+		/* Test if the speed change finished. */
+		if (!(tmp & PORT_LOGIC_SPEED_CHANGE))
+			break;
+		usleep_range(100, 1000);
+	}
+
+	/* Make sure link training is finished as well! */
+	if (count)
+		ret = imx6_pcie_wait_for_link(pp);
+	else
+		ret = -EINVAL;
 
+	if (ret) {
+		dev_err(pp->dev, "Failed to bring link up!\n");
+	} else {
+		tmp = readl(pp->dbi_base + 0x80);
+		dev_dbg(pp->dev, "Link up, Gen=%i\n", (tmp >> 16) & 0xf);
+	}
+
+	return ret;
+}
+
+static void imx6_pcie_host_init(struct pcie_port *pp)
+{
 	imx6_pcie_assert_core_reset(pp);
 
 	imx6_pcie_init_phy(pp);
@@ -336,10 +405,7 @@ static void imx6_pcie_host_init(struct pcie_port *pp)
 
 	dw_pcie_setup_rc(pp);
 
-	regmap_update_bits(imx6_pcie->iomuxc_gpr, IOMUXC_GPR12,
-			IMX6Q_GPR12_PCIE_CTL_2, 1 << 10);
-
-	imx6_pcie_wait_for_link(pp);
+	imx6_pcie_start_link(pp);
 }
 
 static void imx6_pcie_reset_phy(struct pcie_port *pp)