diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
index dd0f98cba0ec..7f42fad909d1 100644
--- a/.buildkite/pipeline.yml
+++ b/.buildkite/pipeline.yml
@@ -179,6 +179,7 @@ steps:
           image: "matrixdotorg/sytest-synapse:py35"
           propagate-environment: true
           always-pull: true
+          workdir: "/src"
     retry:
       automatic:
         - exit_status: -1
@@ -199,6 +200,7 @@ steps:
           image: "matrixdotorg/sytest-synapse:py35"
           propagate-environment: true
           always-pull: true
+          workdir: "/src"
     retry:
       automatic:
         - exit_status: -1
@@ -220,6 +222,7 @@ steps:
           image: "matrixdotorg/sytest-synapse:py35"
           propagate-environment: true
           always-pull: true
+          workdir: "/src"
     soft_fail: true
     retry:
       automatic:
diff --git a/changelog.d/5664.misc b/changelog.d/5664.misc
new file mode 100644
index 000000000000..0ca7a0fbd0c7
--- /dev/null
+++ b/changelog.d/5664.misc
@@ -0,0 +1 @@
+Update the sytest BuildKite configuration to checkout Synapse in `/src`.