diff --git a/drivers/pci/controller/pcie-mediatek.c b/drivers/pci/controller/pcie-mediatek.c
index dcfc7408340f..f34d91e495bc 100644
--- a/drivers/pci/controller/pcie-mediatek.c
+++ b/drivers/pci/controller/pcie-mediatek.c
@@ -530,23 +530,27 @@ static void mtk_pcie_enable_msi(struct mtk_pcie_port *port)
 	writel(val, port->base + PCIE_INT_MASK);
 }
 
+static void mtk_pcie_irq_teardown_port(struct mtk_pcie_port *port)
+{
+	irq_set_chained_handler_and_data(port->irq, NULL, NULL);
+
+	if (port->irq_domain)
+		irq_domain_remove(port->irq_domain);
+
+	if (IS_ENABLED(CONFIG_PCI_MSI)) {
+		if (port->inner_domain)
+			irq_domain_remove(port->inner_domain);
+	}
+
+	irq_dispose_mapping(port->irq);
+}
+
 static void mtk_pcie_irq_teardown(struct mtk_pcie *pcie)
 {
 	struct mtk_pcie_port *port, *tmp;
 
-	list_for_each_entry_safe(port, tmp, &pcie->ports, list) {
-		irq_set_chained_handler_and_data(port->irq, NULL, NULL);
-
-		if (port->irq_domain)
-			irq_domain_remove(port->irq_domain);
-
-		if (IS_ENABLED(CONFIG_PCI_MSI)) {
-			if (port->inner_domain)
-				irq_domain_remove(port->inner_domain);
-		}
-
-		irq_dispose_mapping(port->irq);
-	}
+	list_for_each_entry_safe(port, tmp, &pcie->ports, list)
+		mtk_pcie_irq_teardown_port(port);
 }
 
 static int mtk_pcie_intx_map(struct irq_domain *domain, unsigned int irq,
@@ -866,7 +870,7 @@ static int mtk_pcie_startup_port_an7583(struct mtk_pcie_port *port)
 	return mtk_pcie_startup_port_v2(port);
 }
 
-static void mtk_pcie_enable_port(struct mtk_pcie_port *port)
+static int mtk_pcie_enable_port(struct mtk_pcie_port *port)
 {
 	struct mtk_pcie *pcie = port->pcie;
 	struct device *dev = pcie->dev;
@@ -875,7 +879,7 @@ static void mtk_pcie_enable_port(struct mtk_pcie_port *port)
 	err = clk_prepare_enable(port->sys_ck);
 	if (err) {
 		dev_err(dev, "failed to enable sys_ck%d clock\n", port->slot);
-		goto err_sys_clk;
+		return err;
 	}
 
 	err = clk_prepare_enable(port->ahb_ck);
@@ -923,11 +927,15 @@ static void mtk_pcie_enable_port(struct mtk_pcie_port *port)
 		goto err_phy_on;
 	}
 
-	if (!pcie->soc->startup(port))
-		return;
+	err = pcie->soc->startup(port);
+	if (err) {
+		dev_info(dev, "Port%d link down\n", port->slot);
+		goto err_soc_startup;
+	}
 
-	dev_info(dev, "Port%d link down\n", port->slot);
+	return 0;
 
+err_soc_startup:
 	phy_power_off(port->phy);
 err_phy_on:
 	phy_exit(port->phy);
@@ -943,8 +951,8 @@ static void mtk_pcie_enable_port(struct mtk_pcie_port *port)
 	clk_disable_unprepare(port->ahb_ck);
 err_ahb_clk:
 	clk_disable_unprepare(port->sys_ck);
-err_sys_clk:
-	mtk_pcie_port_free(port);
+
+	return err;
 }
 
 static int mtk_pcie_parse_port(struct mtk_pcie *pcie,
@@ -1110,8 +1118,13 @@ static int mtk_pcie_setup(struct mtk_pcie *pcie)
 		return err;
 
 	/* enable each port, and then check link status */
-	list_for_each_entry_safe(port, tmp, &pcie->ports, list)
-		mtk_pcie_enable_port(port);
+	list_for_each_entry_safe(port, tmp, &pcie->ports, list) {
+		err = mtk_pcie_enable_port(port);
+		if (err) {
+			mtk_pcie_irq_teardown_port(port);
+			mtk_pcie_port_free(port);
+		}
+	}
 
 	/* power down PCIe subsys if slots are all empty (link down) */
 	if (list_empty(&pcie->ports))
@@ -1210,14 +1223,18 @@ static int mtk_pcie_resume_noirq(struct device *dev)
 {
 	struct mtk_pcie *pcie = dev_get_drvdata(dev);
 	struct mtk_pcie_port *port, *tmp;
+	int err;
 
 	if (list_empty(&pcie->ports))
 		return 0;
 
 	clk_prepare_enable(pcie->free_ck);
 
-	list_for_each_entry_safe(port, tmp, &pcie->ports, list)
-		mtk_pcie_enable_port(port);
+	list_for_each_entry_safe(port, tmp, &pcie->ports, list) {
+		err = mtk_pcie_enable_port(port);
+		if (err)
+			mtk_pcie_port_free(port);
+	}
 
 	/* In case of EP was removed while system suspend. */
 	if (list_empty(&pcie->ports))