diff --git a/common/ScalingSettings.cpp b/common/ScalingSettings.cpp
index a91aa1ff..866d48a4 100644
--- a/common/ScalingSettings.cpp
+++ b/common/ScalingSettings.cpp
@@ -115,6 +115,15 @@ ScalingSettings &ScalingSettings::MinCCForImage(double input) {
     return *this;
 }
 
+double ScalingSettings::GetOutlierRejectNsigma() const {
+    return outlier_reject_nsigma;
+}
+
+ScalingSettings &ScalingSettings::OutlierRejectNsigma(double input) {
+    outlier_reject_nsigma = input; // <= 0 disables; no upper bound (large = effectively off)
+    return *this;
+}
+
 double ScalingSettings::GetMinPartiality() const {
     return min_partiality;
 }
diff --git a/common/ScalingSettings.h b/common/ScalingSettings.h
index f7c724f8..6d548cfc 100644
--- a/common/ScalingSettings.h
+++ b/common/ScalingSettings.h
@@ -23,6 +23,7 @@ class ScalingSettings {
     std::optional<double> wedge_for_scaling;
     double min_partiality = 0.02;
     double min_cc_for_image = 0.0;
+    double outlier_reject_nsigma = 6.0; // per-observation merge outlier rejection (XDS/DIALS-style); <= 0 disables
 
     double rfree_fraction = 0.05;
     IntensityFormat intensity_format = IntensityFormat::MTZ;
@@ -37,6 +38,7 @@ public:
     ScalingSettings& HighResolutionLimit_A(double limit);
     ScalingSettings& MinPartiality(double min_partiality);
     ScalingSettings& MinCCForImage(double min_cc_for_image);
+    ScalingSettings& OutlierRejectNsigma(double input);
 
     ScalingSettings& RfreeFraction(double input);
     ScalingSettings& FileFormat(IntensityFormat input);
@@ -63,6 +65,7 @@ public:
 
     [[nodiscard]] double GetMinPartiality() const;
     [[nodiscard]] double GetMinCCForImage() const;
+    [[nodiscard]] double GetOutlierRejectNsigma() const;
 
     [[nodiscard]] double GetRfreeFraction() const;
     [[nodiscard]] IntensityFormat GetFileFormat() const;
diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index 08f875ba..d604e092 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -31,7 +31,9 @@ MergeOnTheFly::MergeOnTheFly(const DiffractionExperiment &x)
                          ? std::optional<double>(scaling_settings.GetMinCCForImage())
                          : std::nullopt),
       min_partiality(scaling_settings.GetMinPartiality()),
-      generator(scaling_settings.GetMergeFriedel(), space_group_number) {
+      generator(scaling_settings.GetMergeFriedel(), space_group_number),
+      reject_outliers(scaling_settings.GetOutlierRejectNsigma() > 0.0),
+      reject_nsigma(scaling_settings.GetOutlierRejectNsigma()) {
 }
 
 MergeOnTheFly &MergeOnTheFly::ReferenceCell(const std::optional<UnitCell> &cell) {
@@ -172,8 +174,8 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
         const double mean = sum_wI / sum_w;
         error_model_mean_I[key] = static_cast<float>(mean);
         // Robust centre for outlier rejection: the median intensity (resists the very
-        // outliers the inverse-variance mean is being protected from).
-        {
+        // outliers the inverse-variance mean is being protected from). Only when active.
+        if (reject_outliers) {
             std::vector<float> iv;
             iv.reserve(obs.size());
             for (const auto &o: obs)
diff --git a/image_analysis/scale_merge/Merge.h b/image_analysis/scale_merge/Merge.h
index a1ea2776..ab9877f4 100644
--- a/image_analysis/scale_merge/Merge.h
+++ b/image_analysis/scale_merge/Merge.h
@@ -109,8 +109,7 @@ public:
     [[nodiscard]] double ErrorModelA() const { return error_model_a; }
     [[nodiscard]] double ErrorModelB() const { return error_model_b; }
 
-    // Enable per-observation outlier rejection (call after RefineErrorModel, before AddImage).
-    void SetRejectOutliers(double nsigma) { reject_outliers = true; reject_nsigma = nsigma; }
+    // Outlier rejection (driven by ScalingSettings::GetOutlierRejectNsigma) reports its count.
     [[nodiscard]] size_t RejectedCount() const { return reject_count; }
 
     void AddImage(const IntegrationOutcome& outcome, bool cc_mask = false);
diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index ef847d86..93ade850 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -72,6 +72,7 @@ void print_usage() {
     std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
     std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
     std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
+    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: 6; 0 disables)" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
     std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
@@ -97,7 +98,8 @@ enum {
     OPT_REDO_ROTATION_SPOTS,
     OPT_FORCE_ROTATION_LATTICE,
     OPT_BANDWIDTH,
-    OPT_INTEGRATION_RADIUS
+    OPT_INTEGRATION_RADIUS,
+    OPT_REJECT_OUTLIERS
 };
 
 static option long_options[] = {
@@ -135,6 +137,7 @@ static option long_options[] = {
     {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
     {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
     {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
+    {"reject-outliers", required_argument, nullptr, OPT_REJECT_OUTLIERS},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -316,6 +319,7 @@ int main(int argc, char **argv) {
     float d_min_spot_finding = 1.5;
     std::optional<float> d_min_scale_merge;
     std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
+    std::optional<double> outlier_reject_nsigma;       // merge per-observation outlier rejection
 
     if (argc == 1) {
         print_usage();
@@ -508,6 +512,9 @@ int main(int argc, char **argv) {
         case OPT_INTEGRATION_RADIUS:
             integration_radius_arg = optarg;
             break;
+        case OPT_REJECT_OUTLIERS:
+            outlier_reject_nsigma = std::stod(optarg);
+            break;
         case OPT_MIN_IMAGE_CC:
             min_image_cc = std::stod(optarg);
             break;
@@ -674,6 +681,8 @@ int main(int argc, char **argv) {
         scaling_settings.RotationWedgeForScaling(wedge_for_scaling);
     scaling_settings.MinPartiality(min_partiality);
     scaling_settings.MinCCForImage(min_image_cc);
+    if (outlier_reject_nsigma)
+        scaling_settings.OutlierRejectNsigma(*outlier_reject_nsigma);
     scaling_settings.FileFormat(intensity_format);
 
     experiment.ImportScalingSettings(scaling_settings);
@@ -1034,15 +1043,11 @@ int main(int argc, char **argv) {
             const double isa = (b > 0.0) ? 1.0 / b : std::numeric_limits<double>::infinity();
             logger.Info("Error model: sigma'^2 = {:.3f} sigma^2 + ({:.4f} I)^2   ISa = {:.1f}", a, b, isa);
         }
-        if (const char *rj = std::getenv("PR_REJECT")) { // TEMP A/B: per-observation outlier rejection
-            const double nsig = std::atof(rj);
-            merge_engine.SetRejectOutliers(nsig);
-            logger.Info("Outlier rejection enabled: dropping observations > {:.1f} sigma from the per-reflection median", nsig);
-        }
         for (auto &i : indexer.GetIntegrationOutcome())
             merge_engine.AddImage(i);
         if (merge_engine.RejectedCount() > 0)
-            logger.Info("Outlier rejection removed {} observations", merge_engine.RejectedCount());
+            logger.Info("Outlier rejection (>{:.1f} sigma from the per-reflection median) removed {} observations",
+                        experiment.GetScalingSettings().GetOutlierRejectNsigma(), merge_engine.RejectedCount());
 
         auto merged_reflections = merge_engine.ExportReflections();
         auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer.GetIntegrationOutcome(), reference_data);