diff --git a/artiq/firmware/runtime/kern_hwreq.rs b/artiq/firmware/runtime/kern_hwreq.rs
index a9c67178b..d1e8d2f5c 100644
--- a/artiq/firmware/runtime/kern_hwreq.rs
+++ b/artiq/firmware/runtime/kern_hwreq.rs
@@ -319,7 +319,7 @@ pub fn process_kern_hwreq(io: &Io, request: &kern::Message) -> io::Result<bool>
     match request {
         &kern::RtioInitRequest => {
             info!("resetting RTIO");
-            rtio_mgt::init_core();
+            rtio_mgt::init_core(false);
             kern_acknowledge()
         }
 
diff --git a/artiq/firmware/runtime/rtio_mgt.rs b/artiq/firmware/runtime/rtio_mgt.rs
index ce89d18a2..6bfef150d 100644
--- a/artiq/firmware/runtime/rtio_mgt.rs
+++ b/artiq/firmware/runtime/rtio_mgt.rs
@@ -244,14 +244,16 @@ pub fn startup(io: &Io) {
     }
 
     drtio::startup(io);
-    init_core();
+    init_core(true);
     io.spawn(4096, async_error_thread);
 }
 
-pub fn init_core() {
+pub fn init_core(phy: bool) {
     unsafe {
         csr::rtio_core::reset_write(1);
-        csr::rtio_core::reset_phy_write(1);
+        if phy {
+            csr::rtio_core::reset_phy_write(1);
+        }
     }
     drtio::init()
 }