diff --git a/drivers/pci/controller/dwc/pci-imx6.c b/drivers/pci/controller/dwc/pci-imx6.c
index 2c05f2f7d1c0b..67dbf9d88d222 100644
--- a/drivers/pci/controller/dwc/pci-imx6.c
+++ b/drivers/pci/controller/dwc/pci-imx6.c
@@ -403,6 +403,11 @@ static void imx6_pcie_assert_core_reset(struct imx6_pcie *imx6_pcie)
 			dev_err(dev, "failed to disable vpcie regulator: %d\n",
 				ret);
 	}
+
+	/* Some boards don't have PCIe reset GPIO. */
+	if (gpio_is_valid(imx6_pcie->reset_gpio))
+		gpio_set_value_cansleep(imx6_pcie->reset_gpio,
+					imx6_pcie->gpio_active_high);
 }
 
 static unsigned int imx6_pcie_grp_offset(const struct imx6_pcie *imx6_pcie)
@@ -525,15 +530,6 @@ static void imx6_pcie_deassert_core_reset(struct imx6_pcie *imx6_pcie)
 	/* allow the clocks to stabilize */
 	usleep_range(200, 500);
 
-	/* Some boards don't have PCIe reset GPIO. */
-	if (gpio_is_valid(imx6_pcie->reset_gpio)) {
-		gpio_set_value_cansleep(imx6_pcie->reset_gpio,
-					imx6_pcie->gpio_active_high);
-		msleep(100);
-		gpio_set_value_cansleep(imx6_pcie->reset_gpio,
-					!imx6_pcie->gpio_active_high);
-	}
-
 	switch (imx6_pcie->drvdata->variant) {
 	case IMX8MQ:
 		reset_control_deassert(imx6_pcie->pciephy_reset);
@@ -576,6 +572,15 @@ static void imx6_pcie_deassert_core_reset(struct imx6_pcie *imx6_pcie)
 		break;
 	}
 
+	/* Some boards don't have PCIe reset GPIO. */
+	if (gpio_is_valid(imx6_pcie->reset_gpio)) {
+		msleep(100);
+		gpio_set_value_cansleep(imx6_pcie->reset_gpio,
+					!imx6_pcie->gpio_active_high);
+		/* Wait for 100ms after PERST# deassertion (PCIe r5.0, 6.6.1) */
+		msleep(100);
+	}
+
 	return;
 
 err_ref_clk: