diff --git a/drivers/spi/atmel-quadspi.c b/drivers/spi/atmel-quadspi.c
index af0464999af1..bf7999ac22c8 100644
--- a/drivers/spi/atmel-quadspi.c
+++ b/drivers/spi/atmel-quadspi.c
@@ -375,9 +375,9 @@ static int atmel_qspi_set_cfg(struct atmel_qspi *aq,
 	 * If the QSPI controller is set in regular SPI mode, set it in
 	 * Serial Memory Mode (SMM).
 	 */
-	if (aq->mr != QSPI_MR_SMM) {
-		atmel_qspi_write(QSPI_MR_SMM, aq, QSPI_MR);
-		aq->mr = QSPI_MR_SMM;
+	if (!(aq->mr & QSPI_MR_SMM)) {
+		aq->mr |= QSPI_MR_SMM;
+		atmel_qspi_write(aq->scr, aq, QSPI_MR);
 	}
 
 	/* Clear pending interrupts */
@@ -501,7 +501,8 @@ static int atmel_qspi_setup(struct spi_device *spi)
 	if (ret < 0)
 		return ret;
 
-	aq->scr = QSPI_SCR_SCBR(scbr);
+	aq->scr &= ~QSPI_SCR_SCBR_MASK;
+	aq->scr |= QSPI_SCR_SCBR(scbr);
 	atmel_qspi_write(aq->scr, aq, QSPI_SCR);
 
 	pm_runtime_mark_last_busy(ctrl->dev.parent);
@@ -534,6 +535,7 @@ static int atmel_qspi_set_cs_timing(struct spi_device *spi)
 	if (ret < 0)
 		return ret;
 
+	aq->scr &= ~QSPI_SCR_DLYBS_MASK;
 	aq->scr |= QSPI_SCR_DLYBS(cs_setup);
 	atmel_qspi_write(aq->scr, aq, QSPI_SCR);
 
@@ -549,8 +551,8 @@ static void atmel_qspi_init(struct atmel_qspi *aq)
 	atmel_qspi_write(QSPI_CR_SWRST, aq, QSPI_CR);
 
 	/* Set the QSPI controller by default in Serial Memory Mode */
-	atmel_qspi_write(QSPI_MR_SMM, aq, QSPI_MR);
-	aq->mr = QSPI_MR_SMM;
+	aq->mr |= QSPI_MR_SMM;
+	atmel_qspi_write(aq->mr, aq, QSPI_MR);
 
 	/* Enable the QSPI controller */
 	atmel_qspi_write(QSPI_CR_QSPIEN, aq, QSPI_CR);