diff --git a/drivers/net/ethernet/stmicro/stmmac/dwmac-socfpga.c b/drivers/net/ethernet/stmicro/stmmac/dwmac-socfpga.c
index 5b3b06a0a3bf..33407df6bea6 100644
--- a/drivers/net/ethernet/stmicro/stmmac/dwmac-socfpga.c
+++ b/drivers/net/ethernet/stmicro/stmmac/dwmac-socfpga.c
@@ -274,16 +274,19 @@ static int socfpga_dwmac_set_phy_mode(struct socfpga_dwmac *dwmac)
 	    phymode == PHY_INTERFACE_MODE_MII ||
 	    phymode == PHY_INTERFACE_MODE_GMII ||
 	    phymode == PHY_INTERFACE_MODE_SGMII) {
-		ctrl |= SYSMGR_EMACGRP_CTRL_PTP_REF_CLK_MASK << (reg_shift / 2);
 		regmap_read(sys_mgr_base_addr, SYSMGR_FPGAGRP_MODULE_REG,
 			    &module);
 		module |= (SYSMGR_FPGAGRP_MODULE_EMAC << (reg_shift / 2));
 		regmap_write(sys_mgr_base_addr, SYSMGR_FPGAGRP_MODULE_REG,
 			     module);
-	} else {
-		ctrl &= ~(SYSMGR_EMACGRP_CTRL_PTP_REF_CLK_MASK << (reg_shift / 2));
 	}
 
+	if (dwmac->f2h_ptp_ref_clk)
+		ctrl |= SYSMGR_EMACGRP_CTRL_PTP_REF_CLK_MASK << (reg_shift / 2);
+	else
+		ctrl &= ~(SYSMGR_EMACGRP_CTRL_PTP_REF_CLK_MASK <<
+			  (reg_shift / 2));
+
 	regmap_write(sys_mgr_base_addr, reg_offset, ctrl);
 
 	/* Deassert reset for the phy configuration to be sampled by