diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6d2681fb..7e5747c2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ version 6.0.0-dev
 + Use softlinks to localise the database for centrifuge.
 + Added the FastqFilter task.
 + Added a new input `revcomp` to cutadapt to set the `--revcomp` flag, defaults to `false`.
++ Fixed bug whereby `samtools.Fastq` could produce out of sync R1/R2 when used with an unsorted bam input. `samtools collate` is now used by default to group reads by readname in order to avoid this issue.
 + New samtools task: split.
 + Update `bedtools.Intersect` to support `-wa`, `-wb`, and `-s` flags.
 
diff --git a/samtools.wdl b/samtools.wdl
index 2020840b..f6c0bb70 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -174,6 +174,7 @@ task Fastq {
     command {
         set -e
         mkdir -p "$(dirname ~{outputRead1})"
+        samtools collate -u -O ~{inputBam} | \
         samtools fastq \
         ~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
         ~{"-2 " + outputRead2} \
@@ -184,8 +185,7 @@ task Fastq {
         ~{true="-N" false="-n" appendReadNumber} \
         ~{true="-O" false="" outputQuality} \
         ~{"-c " + compressionLevel} \
-        ~{"--threads " + threads} \
-        ~{inputBam}
+        ~{"--threads " + threads}
     }
 
     output {