diff --git a/drivers/pci/controller/pci-aardvark.c b/drivers/pci/controller/pci-aardvark.c
index 389ebba1dd9b..d7db03da4d1c 100644
--- a/drivers/pci/controller/pci-aardvark.c
+++ b/drivers/pci/controller/pci-aardvark.c
@@ -31,9 +31,6 @@
 /* PCIe core registers */
 #define PCIE_CORE_DEV_ID_REG					0x0
 #define PCIE_CORE_CMD_STATUS_REG				0x4
-#define     PCIE_CORE_CMD_IO_ACCESS_EN				BIT(0)
-#define     PCIE_CORE_CMD_MEM_ACCESS_EN				BIT(1)
-#define     PCIE_CORE_CMD_MEM_IO_REQ_EN				BIT(2)
 #define PCIE_CORE_DEV_REV_REG					0x8
 #define PCIE_CORE_PCIEXP_CAP					0xc0
 #define PCIE_CORE_ERR_CAPCTL_REG				0x118
@@ -514,6 +511,11 @@ static void advk_pcie_setup_hw(struct advk_pcie *pcie)
 	reg = (PCI_VENDOR_ID_MARVELL << 16) | PCI_VENDOR_ID_MARVELL;
 	advk_writel(pcie, reg, VENDOR_ID_REG);
 
+	/* Disable Root Bridge I/O space, memory space and bus mastering */
+	reg = advk_readl(pcie, PCIE_CORE_CMD_STATUS_REG);
+	reg &= ~(PCI_COMMAND_IO | PCI_COMMAND_MEMORY | PCI_COMMAND_MASTER);
+	advk_writel(pcie, reg, PCIE_CORE_CMD_STATUS_REG);
+
 	/* Set Advanced Error Capabilities and Control PF0 register */
 	reg = PCIE_CORE_ERR_CAPCTL_ECRC_CHK_TX |
 		PCIE_CORE_ERR_CAPCTL_ECRC_CHK_TX_EN |
@@ -612,19 +614,6 @@ static void advk_pcie_setup_hw(struct advk_pcie *pcie)
 		advk_pcie_disable_ob_win(pcie, i);
 
 	advk_pcie_train_link(pcie);
-
-	/*
-	 * FIXME: The following register update is suspicious. This register is
-	 * applicable only when the PCI controller is configured for Endpoint
-	 * mode, not as a Root Complex. But apparently when this code is
-	 * removed, some cards stop working. This should be investigated and
-	 * a comment explaining this should be put here.
-	 */
-	reg = advk_readl(pcie, PCIE_CORE_CMD_STATUS_REG);
-	reg |= PCIE_CORE_CMD_MEM_ACCESS_EN |
-		PCIE_CORE_CMD_IO_ACCESS_EN |
-		PCIE_CORE_CMD_MEM_IO_REQ_EN;
-	advk_writel(pcie, reg, PCIE_CORE_CMD_STATUS_REG);
 }
 
 static int advk_pcie_check_pio_status(struct advk_pcie *pcie, bool allow_crs, u32 *val)
@@ -753,6 +742,37 @@ static int advk_pcie_wait_pio(struct advk_pcie *pcie)
 	return -ETIMEDOUT;
 }
 
+static pci_bridge_emul_read_status_t
+advk_pci_bridge_emul_base_conf_read(struct pci_bridge_emul *bridge,
+				    int reg, u32 *value)
+{
+	struct advk_pcie *pcie = bridge->data;
+
+	switch (reg) {
+	case PCI_COMMAND:
+		*value = advk_readl(pcie, PCIE_CORE_CMD_STATUS_REG);
+		return PCI_BRIDGE_EMUL_HANDLED;
+
+	default:
+		return PCI_BRIDGE_EMUL_NOT_HANDLED;
+	}
+}
+
+static void
+advk_pci_bridge_emul_base_conf_write(struct pci_bridge_emul *bridge,
+				     int reg, u32 old, u32 new, u32 mask)
+{
+	struct advk_pcie *pcie = bridge->data;
+
+	switch (reg) {
+	case PCI_COMMAND:
+		advk_writel(pcie, new, PCIE_CORE_CMD_STATUS_REG);
+		break;
+
+	default:
+		break;
+	}
+}
 
 static pci_bridge_emul_read_status_t
 advk_pci_bridge_emul_pcie_conf_read(struct pci_bridge_emul *bridge,
@@ -854,6 +874,8 @@ advk_pci_bridge_emul_pcie_conf_write(struct pci_bridge_emul *bridge,
 }
 
 static struct pci_bridge_emul_ops advk_pci_bridge_emul_ops = {
+	.read_base = advk_pci_bridge_emul_base_conf_read,
+	.write_base = advk_pci_bridge_emul_base_conf_write,
 	.read_pcie = advk_pci_bridge_emul_pcie_conf_read,
 	.write_pcie = advk_pci_bridge_emul_pcie_conf_write,
 };