diff --git a/av1/encoder/encoder.h b/av1/encoder/encoder.h
index 98bcb6e..538cc46 100644
--- a/av1/encoder/encoder.h
+++ b/av1/encoder/encoder.h
@@ -3188,6 +3188,16 @@
   return lag_in_frames >= ALT_MIN_LAG && enable_auto_arf;
 }
 
+static AOM_INLINE int can_disable_altref(const GFConfig *gf_cfg) {
+  return is_altref_enabled(gf_cfg->lag_in_frames, gf_cfg->enable_auto_arf) &&
+         (gf_cfg->gf_min_pyr_height == 0);
+}
+
+static AOM_INLINE int use_ml_model_to_decide_flat_gop(
+    const RateControlCfg *rc_cfg) {
+  return (rc_cfg->mode == AOM_Q && rc_cfg->cq_level <= 200);
+}
+
 // Check if statistics generation stage
 static INLINE int is_stat_generation_stage(const AV1_COMP *const cpi) {
   assert(IMPLIES(cpi->compressor_stage == LAP_STAGE,
diff --git a/av1/encoder/firstpass.c b/av1/encoder/firstpass.c
index dd0f8af..52dc514 100644
--- a/av1/encoder/firstpass.c
+++ b/av1/encoder/firstpass.c
@@ -54,6 +54,8 @@
 #define NCOUNT_INTRA_THRESH 8192
 #define NCOUNT_INTRA_FACTOR 3
 
+#define INVALID_FP_STATS_TO_PREDICT_FLAT_GOP -1
+
 static AOM_INLINE void output_stats(FIRSTPASS_STATS *stats,
                                     struct aom_codec_pkt_list *pktlist) {
   struct aom_codec_cx_pkt pkt;
@@ -121,9 +123,11 @@
   section->frame_avg_wavelet_energy += frame->frame_avg_wavelet_energy;
   section->coded_error += frame->coded_error;
   section->sr_coded_error += frame->sr_coded_error;
+  section->tr_coded_error += frame->tr_coded_error;
   section->pcnt_inter += frame->pcnt_inter;
   section->pcnt_motion += frame->pcnt_motion;
   section->pcnt_second_ref += frame->pcnt_second_ref;
+  section->pcnt_third_ref += frame->pcnt_third_ref;
   section->pcnt_neutral += frame->pcnt_neutral;
   section->intra_skip_pct += frame->intra_skip_pct;
   section->inactive_zone_rows += frame->inactive_zone_rows;
@@ -356,6 +360,11 @@
   return raw_err_stdev;
 }
 
+static AOM_INLINE int do_third_ref_motion_search(const RateControlCfg *rc_cfg,
+                                                 const GFConfig *gf_cfg) {
+  return use_ml_model_to_decide_flat_gop(rc_cfg) && can_disable_altref(gf_cfg);
+}
+
 #define UL_INTRA_THRESH 50
 #define INVALID_ROW -1
 // Computes and returns the intra pred error of a block.
@@ -682,14 +691,22 @@
 
     // Motion search in 3rd reference frame.
     int alt_motion_error = motion_error;
-    if (alt_ref_frame != NULL) {
-      FULLPEL_MV tmp_mv = kZeroFullMv;
-      xd->plane[0].pre[0].buf = alt_ref_frame->y_buffer + alt_ref_frame_yoffset;
-      xd->plane[0].pre[0].stride = alt_ref_frame->y_stride;
-      alt_motion_error =
-          get_prediction_error_bitdepth(is_high_bitdepth, bitdepth, bsize,
-                                        &x->plane[0].src, &xd->plane[0].pre[0]);
-      first_pass_motion_search(cpi, x, &kZeroMv, &tmp_mv, &alt_motion_error);
+    // The ML model to predict if a flat structure (golden-frame only structure
+    // without ALT-REF and Internal-ARFs) is better requires stats based on
+    // motion search w.r.t 3rd reference frame in the first pass. As the ML
+    // model is enabled under certain conditions, motion search in 3rd reference
+    // frame is also enabled for those cases.
+    if (do_third_ref_motion_search(&cpi->oxcf.rc_cfg, &cpi->oxcf.gf_cfg)) {
+      if (alt_ref_frame != NULL) {
+        FULLPEL_MV tmp_mv = kZeroFullMv;
+        xd->plane[0].pre[0].buf =
+            alt_ref_frame->y_buffer + alt_ref_frame_yoffset;
+        xd->plane[0].pre[0].stride = alt_ref_frame->y_stride;
+        alt_motion_error = get_prediction_error_bitdepth(
+            is_high_bitdepth, bitdepth, bsize, &x->plane[0].src,
+            &xd->plane[0].pre[0]);
+        first_pass_motion_search(cpi, x, &kZeroMv, &tmp_mv, &alt_motion_error);
+      }
     }
     if (alt_motion_error < motion_error && alt_motion_error < gf_motion_error &&
         alt_motion_error < this_intra_error) {
@@ -851,6 +868,13 @@
   // cpi->source_time_stamp.
   fps.duration = (double)ts_duration;
 
+  // Invalidate the stats related to third ref motion search if not valid.
+  // This helps to print a warning in second pass encoding.
+  if (do_third_ref_motion_search(&cpi->oxcf.rc_cfg, &cpi->oxcf.gf_cfg) == 0) {
+    fps.pcnt_third_ref = INVALID_FP_STATS_TO_PREDICT_FLAT_GOP;
+    fps.tr_coded_error = INVALID_FP_STATS_TO_PREDICT_FLAT_GOP;
+  }
+
   // We will store the stats inside the persistent twopass struct (and NOT the
   // local variable 'fps'), and then cpi->output_pkt_list will point to it.
   *this_frame_stats = fps;
diff --git a/av1/encoder/pass2_strategy.c b/av1/encoder/pass2_strategy.c
index f7e03db..9dbdfb2 100644
--- a/av1/encoder/pass2_strategy.c
+++ b/av1/encoder/pass2_strategy.c
@@ -19,6 +19,7 @@
 
 #include <stdint.h>
 
+#include "common/tools_common.h"
 #include "config/aom_config.h"
 #include "config/aom_scale_rtcd.h"
 
@@ -43,6 +44,10 @@
 #define DEFAULT_KF_BOOST 2300
 #define DEFAULT_GF_BOOST 2000
 #define GROUP_ADAPTIVE_MAXQ 1
+
+#define IS_FP_STATS_TO_PREDICT_FLAT_GOP_INVALID(fp_stats) \
+  (((fp_stats)->tr_coded_error < 0) || ((fp_stats)->pcnt_third_ref < 0))
+
 static void init_gf_stats(GF_GROUP_STATS *gf_stats);
 
 // Calculate an active area of the image that discounts formatting
@@ -2425,8 +2430,10 @@
         p_rc->use_arf_in_this_kf_group && (i < gf_cfg->lag_in_frames) &&
         (i >= MIN_GF_INTERVAL);
 
+    FIRSTPASS_STATS *total_stats = twopass->stats_buf_ctx->total_stats;
     // TODO(urvang): Improve and use model for VBR, CQ etc as well.
-    if (use_alt_ref && rc_cfg->mode == AOM_Q && rc_cfg->cq_level <= 200) {
+    if (use_alt_ref && use_ml_model_to_decide_flat_gop(rc_cfg) &&
+        !IS_FP_STATS_TO_PREDICT_FLAT_GOP_INVALID(total_stats)) {
       aom_clear_system_state();
       float features[21];
       get_features_from_gf_stats(
@@ -3384,18 +3391,28 @@
   CurrentFrame *const current_frame = &cm->current_frame;
   RATE_CONTROL *const rc = &cpi->rc;
   TWO_PASS *const twopass = &cpi->ppi->twopass;
+  FIRSTPASS_STATS *total_stats = twopass->stats_buf_ctx->total_stats;
+
+  if (current_frame->frame_number == 0) {
+    const GFConfig *const gf_cfg = &cpi->oxcf.gf_cfg;
+    const RateControlCfg *const rc_cfg = &cpi->oxcf.rc_cfg;
+    if (use_ml_model_to_decide_flat_gop(rc_cfg) && can_disable_altref(gf_cfg) &&
+        IS_FP_STATS_TO_PREDICT_FLAT_GOP_INVALID(total_stats))
+      warn(
+          "First pass stats required in the ML model to predict a flat GOP "
+          "structure is invalid. Continuing encoding by disabling the ML "
+          "model.\n");
+  }
 
   if (cpi->oxcf.rc_cfg.mode != AOM_Q && current_frame->frame_number == 0 &&
-      cpi->gf_frame_index == 0 &&
-      cpi->ppi->twopass.stats_buf_ctx->total_stats &&
+      cpi->gf_frame_index == 0 && total_stats &&
       cpi->ppi->twopass.stats_buf_ctx->total_left_stats) {
     if (cpi->ppi->lap_enabled) {
       /*
        * Accumulate total_stats using available limited number of stats,
        * and assign it to total_left_stats.
        */
-      *cpi->ppi->twopass.stats_buf_ctx->total_left_stats =
-          *cpi->ppi->twopass.stats_buf_ctx->total_stats;
+      *cpi->ppi->twopass.stats_buf_ctx->total_left_stats = *total_stats;
     }
     // Special case code for first frame.
     const int section_target_bandwidth = get_section_target_bandwidth(cpi);