diff --git a/fftools/ffmpeg.c b/fftools/ffmpeg.c
index 0e1477299d..fabb0fb952 100644
--- a/fftools/ffmpeg.c
+++ b/fftools/ffmpeg.c
@@ -1898,7 +1898,7 @@ static void do_streamcopy(InputStream *ist, OutputStream *ost, const AVPacket *p
         start_time = 0;
         if (copy_ts) {
             start_time += f->start_time != AV_NOPTS_VALUE ? f->start_time : 0;
-            start_time += start_at_zero ? 0 : f->ctx->start_time;
+            start_time += start_at_zero ? 0 : f->enabled_start_time;
         }
         if (ist->pts >= f->recording_time + start_time) {
             close_output_stream(ost);
@@ -3323,28 +3323,6 @@ static int transcode_init(void)
                 input_streams[j + ifile->ist_index]->start = av_gettime_relative();
     }
 
-    // Correct starttime based on the enabled streams
-    for (i = 0; i < nb_input_files; i++) {
-        InputFile       *ifile = input_files[i];
-        AVFormatContext    *is = ifile->ctx;
-        int64_t new_start_time = INT64_MAX;
-
-        if (is->start_time == AV_NOPTS_VALUE ||
-            !(is->iformat->flags & AVFMT_TS_DISCONT))
-            continue;
-
-        for (int j = 0; j < is->nb_streams; j++) {
-            AVStream *st = is->streams[j];
-            if(st->discard == AVDISCARD_ALL || st->start_time == AV_NOPTS_VALUE)
-                continue;
-            new_start_time = FFMIN(new_start_time, av_rescale_q(st->start_time, st->time_base, AV_TIME_BASE_Q));
-        }
-        if (new_start_time > is->start_time) {
-            av_log(is, AV_LOG_VERBOSE, "Correcting start time by %"PRId64"\n", new_start_time - is->start_time);
-            ifile->ts_offset = -new_start_time;
-        }
-    }
-
     /* init input streams */
     for (i = 0; i < nb_input_streams; i++)
         if ((ret = init_input_stream(i, error, sizeof(error))) < 0)
diff --git a/fftools/ffmpeg.h b/fftools/ffmpeg.h
index ede0b2bd96..b93c2427b6 100644
--- a/fftools/ffmpeg.h
+++ b/fftools/ffmpeg.h
@@ -439,7 +439,10 @@ typedef struct InputFile {
     AVRational time_base; /* time base of the duration */
     int64_t input_ts_offset;
     int input_sync_ref;
-
+    /**
+     * Effective format start time based on enabled streams.
+     */
+    int64_t enabled_start_time;
     int64_t ts_offset;
     /**
      * Extra timestamp offset added by discontinuity handling.
diff --git a/fftools/ffmpeg_demux.c b/fftools/ffmpeg_demux.c
index 6e89f5999a..6125181f81 100644
--- a/fftools/ffmpeg_demux.c
+++ b/fftools/ffmpeg_demux.c
@@ -120,7 +120,7 @@ static int seek_to_start(InputFile *ifile)
 static void ts_fixup(InputFile *ifile, AVPacket *pkt, int *repeat_pict)
 {
     InputStream *ist = input_streams[ifile->ist_index + pkt->stream_index];
-    const int64_t start_time = ifile->ctx->start_time;
+    const int64_t start_time = ifile->enabled_start_time;
     int64_t duration;
 
     if (debug_ts) {
@@ -367,7 +367,7 @@ int ifile_get_packet(InputFile *f, AVPacket **pkt)
     if (f->readrate || f->rate_emu) {
         int i;
         int64_t file_start = copy_ts * (
-                              (f->ctx->start_time != AV_NOPTS_VALUE ? f->ctx->start_time * !start_at_zero : 0) +
+                              (f->enabled_start_time != AV_NOPTS_VALUE ? f->enabled_start_time * !start_at_zero : 0) +
                               (f->start_time != AV_NOPTS_VALUE ? f->start_time : 0)
                              );
         float scale = f->rate_emu ? 1.0 : f->readrate;
diff --git a/fftools/ffmpeg_opt.c b/fftools/ffmpeg_opt.c
index 5febe319e4..8df322c31c 100644
--- a/fftools/ffmpeg_opt.c
+++ b/fftools/ffmpeg_opt.c
@@ -293,6 +293,44 @@ static int parse_and_set_vsync(const char *arg, int *vsync_var, int file_idx, in
     return 0;
 }
 
+/* Correct input file start times based on enabled streams */
+static int correct_input_start_times(void)
+{
+    for (int i = 0; i < nb_input_files; i++) {
+        InputFile       *ifile = input_files[i];
+        AVFormatContext    *is = ifile->ctx;
+        int64_t new_start_time = INT64_MAX, diff, abs_start_seek;
+
+        ifile->enabled_start_time = is->start_time;
+
+        if (is->start_time == AV_NOPTS_VALUE ||
+            !(is->iformat->flags & AVFMT_TS_DISCONT))
+            continue;
+
+        for (int j = 0; j < is->nb_streams; j++) {
+            AVStream *st = is->streams[j];
+            if(st->discard == AVDISCARD_ALL || st->start_time == AV_NOPTS_VALUE)
+                continue;
+            new_start_time = FFMIN(new_start_time, av_rescale_q(st->start_time, st->time_base, AV_TIME_BASE_Q));
+        }
+
+        diff = new_start_time - is->start_time;
+        if (diff) {
+            av_log(NULL, AV_LOG_VERBOSE, "Correcting start time of Input #%d by %"PRId64" us.\n", i, diff);
+            ifile->enabled_start_time = new_start_time;
+            if (copy_ts && start_at_zero)
+                ifile->ts_offset = -new_start_time;
+            else if (!copy_ts) {
+                abs_start_seek = is->start_time + (ifile->start_time != AV_NOPTS_VALUE) ? ifile->start_time : 0;
+                ifile->ts_offset = abs_start_seek > new_start_time ? -abs_start_seek : -new_start_time;
+            }
+            ifile->ts_offset += ifile->input_ts_offset;
+        }
+    }
+
+    return 0;
+}
+
 static int apply_sync_offsets(void)
 {
     for (int i = 0; i < nb_input_files; i++) {
@@ -321,9 +359,9 @@ static int apply_sync_offsets(void)
         if (self->ctx->start_time_realtime != AV_NOPTS_VALUE && ref->ctx->start_time_realtime != AV_NOPTS_VALUE) {
             self_start_time = self->ctx->start_time_realtime;
             ref_start_time  =  ref->ctx->start_time_realtime;
-        } else if (self->ctx->start_time != AV_NOPTS_VALUE && ref->ctx->start_time != AV_NOPTS_VALUE) {
-            self_start_time = self->ctx->start_time;
-            ref_start_time  =  ref->ctx->start_time;
+        } else if (self->enabled_start_time != AV_NOPTS_VALUE && ref->enabled_start_time != AV_NOPTS_VALUE) {
+            self_start_time = self->enabled_start_time;
+            ref_start_time  =  ref->enabled_start_time;
         } else {
             start_times_set = 0;
         }
@@ -3747,8 +3785,6 @@ int ffmpeg_parse_options(int argc, char **argv)
         goto fail;
     }
 
-    apply_sync_offsets();
-
     /* create the complex filtergraphs */
     ret = init_complex_filters();
     if (ret < 0) {
@@ -3763,6 +3799,10 @@ int ffmpeg_parse_options(int argc, char **argv)
         goto fail;
     }
 
+    correct_input_start_times();
+
+    apply_sync_offsets();
+
     check_filter_outputs();
 
 fail:
