diff --git a/drivers/pci/controller/pci-mvebu.c b/drivers/pci/controller/pci-mvebu.c
index 5d5f23b1d355..2e6945540028 100644
--- a/drivers/pci/controller/pci-mvebu.c
+++ b/drivers/pci/controller/pci-mvebu.c
@@ -215,16 +215,14 @@ static void mvebu_pcie_setup_hw(struct mvebu_pcie_port *port)
 {
 	u32 cmd, mask;
 
+	/* Disable Root Bridge I/O space, memory space and bus mastering. */
+	cmd = mvebu_readl(port, PCIE_CMD_OFF);
+	cmd &= ~(PCI_COMMAND_IO | PCI_COMMAND_MEMORY | PCI_COMMAND_MASTER);
+	mvebu_writel(port, cmd, PCIE_CMD_OFF);
+
 	/* Point PCIe unit MBUS decode windows to DRAM space. */
 	mvebu_pcie_setup_wins(port);
 
-	/* Master + slave enable. */
-	cmd = mvebu_readl(port, PCIE_CMD_OFF);
-	cmd |= PCI_COMMAND_IO;
-	cmd |= PCI_COMMAND_MEMORY;
-	cmd |= PCI_COMMAND_MASTER;
-	mvebu_writel(port, cmd, PCIE_CMD_OFF);
-
 	/* Enable interrupt lines A-D. */
 	mask = mvebu_readl(port, PCIE_MASK_OFF);
 	mask |= PCIE_MASK_ENABLE_INTS;
@@ -371,8 +369,7 @@ static void mvebu_pcie_handle_iobase_change(struct mvebu_pcie_port *port)
 
 	/* Are the new iobase/iolimit values invalid? */
 	if (conf->iolimit < conf->iobase ||
-	    conf->iolimitupper < conf->iobaseupper ||
-	    !(conf->command & PCI_COMMAND_IO)) {
+	    conf->iolimitupper < conf->iobaseupper) {
 		mvebu_pcie_set_window(port, port->io_target, port->io_attr,
 				      &desired, &port->iowin);
 		return;
@@ -409,8 +406,7 @@ static void mvebu_pcie_handle_membase_change(struct mvebu_pcie_port *port)
 	struct pci_bridge_emul_conf *conf = &port->bridge.conf;
 
 	/* Are the new membase/memlimit values invalid? */
-	if (conf->memlimit < conf->membase ||
-	    !(conf->command & PCI_COMMAND_MEMORY)) {
+	if (conf->memlimit < conf->membase) {
 		mvebu_pcie_set_window(port, port->mem_target, port->mem_attr,
 				      &desired, &port->memwin);
 		return;
@@ -430,6 +426,24 @@ static void mvebu_pcie_handle_membase_change(struct mvebu_pcie_port *port)
 			      &port->memwin);
 }
 
+static pci_bridge_emul_read_status_t
+mvebu_pci_bridge_emul_base_conf_read(struct pci_bridge_emul *bridge,
+				     int reg, u32 *value)
+{
+	struct mvebu_pcie_port *port = bridge->data;
+
+	switch (reg) {
+	case PCI_COMMAND:
+		*value = mvebu_readl(port, PCIE_CMD_OFF);
+		break;
+
+	default:
+		return PCI_BRIDGE_EMUL_NOT_HANDLED;
+	}
+
+	return PCI_BRIDGE_EMUL_HANDLED;
+}
+
 static pci_bridge_emul_read_status_t
 mvebu_pci_bridge_emul_pcie_conf_read(struct pci_bridge_emul *bridge,
 				     int reg, u32 *value)
@@ -484,17 +498,14 @@ mvebu_pci_bridge_emul_base_conf_write(struct pci_bridge_emul *bridge,
 
 	switch (reg) {
 	case PCI_COMMAND:
-	{
-		if (!mvebu_has_ioport(port))
-			conf->command &= ~PCI_COMMAND_IO;
-
-		if ((old ^ new) & PCI_COMMAND_IO)
-			mvebu_pcie_handle_iobase_change(port);
-		if ((old ^ new) & PCI_COMMAND_MEMORY)
-			mvebu_pcie_handle_membase_change(port);
+		if (!mvebu_has_ioport(port)) {
+			conf->command = cpu_to_le16(
+				le16_to_cpu(conf->command) & ~PCI_COMMAND_IO);
+			new &= ~PCI_COMMAND_IO;
+		}
 
+		mvebu_writel(port, new, PCIE_CMD_OFF);
 		break;
-	}
 
 	case PCI_IO_BASE:
 		mvebu_pcie_handle_iobase_change(port);
@@ -554,6 +565,7 @@ mvebu_pci_bridge_emul_pcie_conf_write(struct pci_bridge_emul *bridge,
 }
 
 static struct pci_bridge_emul_ops mvebu_pci_bridge_emul_ops = {
+	.read_base = mvebu_pci_bridge_emul_base_conf_read,
 	.write_base = mvebu_pci_bridge_emul_base_conf_write,
 	.read_pcie = mvebu_pci_bridge_emul_pcie_conf_read,
 	.write_pcie = mvebu_pci_bridge_emul_pcie_conf_write,