diff --git a/config/federation/prometheus/prometheus.yml.template b/config/federation/prometheus/prometheus.yml.template
index d3cb41ce..b8e86191 100644
--- a/config/federation/prometheus/prometheus.yml.template
+++ b/config/federation/prometheus/prometheus.yml.template
@@ -444,16 +444,56 @@ scrape_configs:
         replacement: ${1}
 
 
-  # script_exporter configurations. The scrape_timeout is set very high because
-  # one of the script_exporter scripts is the NDT end-to-end test, which will
-  # take around 35 seconds.
-  - job_name: 'script-targets'
+  # script_exporter configurations for the ndt_e2e script. The scrape_timeout is
+  # set very high because one of the NDT end-to-end test will take around 35
+  # seconds.
+  - job_name: 'script-targets-ndt-e2e'
     metrics_path: /probe
+    scrape_interval: 10m
     scrape_timeout: 45s
 
     file_sd_configs:
       - files:
-          - /script-targets/*.json
+          - /script-targets/ndt_e2e.json
+        # Attempt to re-read files every five minutes.
+        refresh_interval: 5m
+
+    # This relabel config is necessary. The relabel config redefines the address
+    # to scrape and sets the correct parameters to pass to the scrape target.
+    relabel_configs:
+      # The value of the source label named "service" must match the name of a
+      # configured script in the script_exporter configuration. See this file:
+      # https://github.com/m-lab/prometheus-script-exporter/blob/master/script_exporter.yml
+      - source_labels: [service]
+        regex: (.*)
+        target_label: __param_name
+        replacement: ${1}
+
+      # The default __address__ value is a target host from the config file.
+      # Here, we set (i.e. "replace") a request parameter "target" equal to the
+      # host value.
+      - source_labels: [__address__]
+        regex: (.*)
+        target_label: __param_target
+        replacement: ${1}
+
+      # Since __address__ is the target that prometheus will contact,
+      # unconditionally reset the __address__ label to the script_exporter
+      # address.
+      - source_labels: []
+        regex: .*
+        target_label: __address__
+        replacement: script-exporter.{{PROJECT}}.measurementlab.net:9172
+
+
+  # script_exporter configurations for the ndt_queue script.
+  - job_name: 'script-targets-ndt-queue'
+    metrics_path: /probe
+    scrape_timeout: 15s
+
+    file_sd_configs:
+      - files:
+          - /script-targets/ndt_queue.json
         # Attempt to re-read files every five minutes.
         refresh_interval: 5m