diff --git a/artiq/firmware/libdrtioaux/lib.rs b/artiq/firmware/libdrtioaux/lib.rs
index 7074d3a09..927825630 100644
--- a/artiq/firmware/libdrtioaux/lib.rs
+++ b/artiq/firmware/libdrtioaux/lib.rs
@@ -17,6 +17,8 @@ use proto::*;
 pub enum Packet {
     EchoRequest,
     EchoReply,
+    ResetRequest { phy: bool },
+    ResetAck,
 
     RtioErrorRequest,
     RtioNoErrorReply,
@@ -52,6 +54,10 @@ impl Packet {
         Ok(match read_u8(reader)? {
             0x00 => Packet::EchoRequest,
             0x01 => Packet::EchoReply,
+            0x02 => Packet::ResetRequest {
+                phy: read_bool(reader)?
+            },
+            0x03 => Packet::ResetAck,
 
             0x20 => Packet::RtioErrorRequest,
             0x21 => Packet::RtioNoErrorReply,
@@ -149,6 +155,11 @@ impl Packet {
         match *self {
             Packet::EchoRequest => write_u8(writer, 0x00)?,
             Packet::EchoReply => write_u8(writer, 0x01)?,
+            Packet::ResetRequest { phy } => {
+                write_u8(writer, 0x02)?;
+                write_bool(writer, phy)?;
+            },
+            Packet::ResetAck => write_u8(writer, 0x03)?,
 
             Packet::RtioErrorRequest => write_u8(writer, 0x20)?,
             Packet::RtioNoErrorReply => write_u8(writer, 0x21)?,
diff --git a/artiq/firmware/runtime/rtio_mgt.rs b/artiq/firmware/runtime/rtio_mgt.rs
index bc03eac5d..f05c99d09 100644
--- a/artiq/firmware/runtime/rtio_mgt.rs
+++ b/artiq/firmware/runtime/rtio_mgt.rs
@@ -131,21 +131,34 @@ pub mod drtio {
             Err(e) => error!("[LINK#{}] aux packet error ({})", linkno, e)
         }
     }
+    
+    // FIXME: use csr::DRTIO.len(), maybe get rid of static mut as well.
+    static mut LINK_UP: [bool; 16] = [false; 16];
+
+    fn link_up(linkno: u8) -> bool {
+        unsafe {
+            LINK_UP[linkno as usize]
+        }
+    }
+
+    fn set_link_up(linkno: u8, up: bool) {
+        unsafe {
+            LINK_UP[linkno as usize] = up
+        }
+    }
 
     pub fn link_thread(io: Io) {
-        let mut link_up = vec![false; csr::DRTIO.len()];
-
         loop {
             for linkno in 0..csr::DRTIO.len() {
                 let linkno = linkno as u8;
-                if link_up[linkno as usize] {
+                if link_up(linkno) {
                     /* link was previously up */
                     if link_rx_up(linkno) {
                         process_local_errors(linkno);
                         process_aux_errors(linkno);
                     } else {
                         info!("[LINK#{}] link is down", linkno);
-                        link_up[linkno as usize] = false;
+                        set_link_up(linkno, false);
                     }
                 } else {
                     /* link was previously down */
@@ -158,7 +171,7 @@ pub mod drtio {
                             init_buffer_space(linkno);
                             sync_tsc(linkno);
                             info!("[LINK#{}] link initialization completed", linkno);
-                            link_up[linkno as usize] = true;
+                            set_link_up(linkno, true);
                         } else {
                             info!("[LINK#{}] ping failed", linkno);
                         }
@@ -170,7 +183,18 @@ pub mod drtio {
     }
 
     pub fn init() {
-        // TODO: send reset commands (over aux) to every link that is up
+        for linkno in 0..csr::DRTIO.len() {
+            let linkno = linkno as u8;
+            if link_up(linkno) {
+                drtioaux::hw::send_link(linkno,
+                    &drtioaux::Packet::ResetRequest { phy: false }).unwrap();
+                match drtioaux::hw::recv_timeout_link(linkno, None) {
+                    Ok(drtioaux::Packet::ResetAck) => (),
+                    Ok(_) => error!("[LINK#{}] reset failed, received unexpected aux packet", linkno),
+                    Err(e) => error!("[LINK#{}] reset failed, aux packet error ({})", linkno, e)
+                }
+            }
+        }
     }
 }
 
diff --git a/artiq/firmware/satman/main.rs b/artiq/firmware/satman/main.rs
index 77c63f0ef..2e11ad869 100644
--- a/artiq/firmware/satman/main.rs
+++ b/artiq/firmware/satman/main.rs
@@ -18,11 +18,33 @@ use board_artiq::serwb;
 #[cfg(has_hmc830_7043)]
 use board_artiq::hmc830_7043;
 
+
+fn drtio_reset(reset: bool) {
+    unsafe {
+        (csr::DRTIO[0].reset_write)(if reset { 1 } else { 0 });
+    }
+}
+
+fn drtio_reset_phy(reset: bool) {
+    unsafe {
+        (csr::DRTIO[0].reset_phy_write)(if reset { 1 } else { 0 });
+    }
+}
+
 fn process_aux_packet(p: &drtioaux::Packet) {
     // In the code below, *_chan_sel_write takes an u8 if there are fewer than 256 channels,
     // and u16 otherwise; hence the `as _` conversion.
     match *p {
         drtioaux::Packet::EchoRequest => drtioaux::hw::send_link(0, &drtioaux::Packet::EchoReply).unwrap(),
+        drtioaux::Packet::ResetRequest { phy } => {
+            if phy {
+                drtio_reset_phy(true);
+                drtio_reset_phy(false);
+            } else {
+                drtio_reset(true);
+                drtio_reset(false);
+            }
+        },
 
         drtioaux::Packet::RtioErrorRequest => {
             let errors;
@@ -193,14 +215,6 @@ fn drtio_link_is_up() -> bool {
     }
 }
 
-fn drtio_reset(reset: bool) {
-    let reset = if reset { 1 } else { 0 };
-    unsafe {
-        (csr::DRTIO[0].reset_write)(reset);
-        (csr::DRTIO[0].reset_phy_write)(reset);
-    }
-}
-
 fn startup() {
     board::clock::init();
     info!("ARTIQ satellite manager starting...");
@@ -225,10 +239,12 @@ fn startup() {
         info!("link is up, switching to recovered clock");
         si5324::select_ext_input(true).expect("failed to switch clocks");
         drtio_reset(false);
+        drtio_reset_phy(false);
         while drtio_link_is_up() {
             process_errors();
             process_aux_packets();
         }
+        drtio_reset_phy(true);
         drtio_reset(true);
         info!("link is down, switching to local crystal clock");
         si5324::select_ext_input(false).expect("failed to switch clocks");