diff --git a/drivers/pci/host/pci-mvebu.c b/drivers/pci/host/pci-mvebu.c
index 0d638b7..7b7d19a 100644
--- a/drivers/pci/host/pci-mvebu.c
+++ b/drivers/pci/host/pci-mvebu.c
@@ -21,6 +21,7 @@
 #include <linux/of_gpio.h>
 #include <linux/of_pci.h>
 #include <linux/of_platform.h>
+#include <linux/clk-provider.h>
 
 /*
  * PCIe unit register offsets.
@@ -973,6 +974,7 @@ static int mvebu_pcie_probe(struct platform_device *pdev)
 	for_each_child_of_node(pdev->dev.of_node, child) {
 		struct mvebu_pcie_port *port = &pcie->ports[i];
 		enum of_gpio_flags flags;
+		bool enabled;
 
 		if (!of_device_is_available(child))
 			continue;
@@ -1044,6 +1046,9 @@ static int mvebu_pcie_probe(struct platform_device *pdev)
 			continue;
 		}
 
+		// Does this work on MVEBU?
+		enabled = __clk_is_enabled(port->clk);
+
 		ret = clk_prepare_enable(port->clk);
 		if (ret)
 			continue;
@@ -1057,7 +1062,35 @@ static int mvebu_pcie_probe(struct platform_device *pdev)
 			continue;
 		}
 
-		mvebu_pcie_set_local_dev_nr(port, 1);
+		if (!enabled) {
+			u32 reg;
+			unsigned int tries;
+
+			/* The clock is being turned on for the first time, do
+			 * a PHY reset
+			 */
+			dev_info(&pdev->dev,
+				 "PCIe%d.%d: performing link reset\n",
+				 port->port, port->lane);
+			reg = mvebu_readl(port, PCIE_CTRL_OFF);
+			mvebu_writel(port,
+				     reg & ~BIT(30), // Conf_TrainingDisable
+				     PCIE_CTRL_OFF);
+			do {
+				udelay(100); // Guess?
+			} while (mvebu_pcie_link_up(port));
+			mvebu_pcie_set_local_dev_nr(port, 1);
+			mvebu_writel(port, reg | ~BIT(30), PCIE_CTRL_OFF);
+
+			for (tries = 0;
+			     !mvebu_pcie_link_up(port) && tries != 100; tries++)
+				udelay(100);
+		} else {
+			/* We expect the bootloader has setup the port and
+			 * waited for the link to go up
+			 */
+			mvebu_pcie_set_local_dev_nr(port, 1);
+		}
 
 		port->dn = child;
 		spin_lock_init(&port->conf_lock);