diff --git a/app/services/riiif/imagemagick_command_factory.rb b/app/services/riiif/imagemagick_command_factory.rb
index 55d8d3d..1e03787 100644
--- a/app/services/riiif/imagemagick_command_factory.rb
+++ b/app/services/riiif/imagemagick_command_factory.rb
@@ -14,20 +14,36 @@ class ImagemagickCommandFactory
     # @param [Integer] compression (85) the compression level to use (set 0 for no compression)
     # @param [String] sampling_factor ("4:2:0") the chroma sample factor (set 0 for no compression)
     # @param [Boolean] strip_metadata (true) do we want to strip EXIF tags?
-    def initialize(path, info, transformation, compression: 85, sampling_factor: '4:2:0', strip_metadata: true)
+    # @param [Boolean] flatten (true) do we want to flatten the image/PDF layers?
+    def initialize(path, info, transformation, compression: 85,
+                   sampling_factor: '4:2:0', strip_metadata: true, flatten: true)
       @path = path
       @info = info
       @transformation = transformation
       @compression = compression
       @sampling_factor = sampling_factor
       @strip_metadata = strip_metadata
+      @flatten = flatten
     end
 
-    attr_reader :path, :info, :transformation, :compression, :sampling_factor, :strip_metadata
+    attr_reader :path, :info, :transformation, :compression,
+                :sampling_factor, :strip_metadata, :flatten
 
     # @return [String] a command for running imagemagick to produce the requested output
     def command
-      [external_command, crop, size, rotation, colorspace, quality, sampling, metadata, input, output].join
+      [
+        external_command,
+        crop,
+        size,
+        rotation,
+        colorspace,
+        quality,
+        sampling,
+        metadata,
+        flatten_layers,
+        input,
+        output
+      ].join
     end
 
     def reduction_factor
@@ -88,5 +104,9 @@ def colorspace
           ' -colorspace Gray -type Bilevel'
         end
       end
+
+      def flatten_layers
+        ' -flatten' if flatten
+      end
   end
 end
diff --git a/spec/models/riiif/image_spec.rb b/spec/models/riiif/image_spec.rb
index cffcbe4..ebaf7f6 100644
--- a/spec/models/riiif/image_spec.rb
+++ b/spec/models/riiif/image_spec.rb
@@ -20,7 +20,7 @@
 
     it 'renders' do
       expect(Riiif::CommandRunner).to receive(:execute)
-        .with("convert -quality 85 -sampling-factor 4:2:0 -strip #{filename} jpg:-")
+        .with("convert -quality 85 -sampling-factor 4:2:0 -strip -flatten #{filename} jpg:-")
         .and_return('imagedata')
 
       expect(subject.render('size' => 'full', format: 'jpg')).to eq 'imagedata'
@@ -82,7 +82,7 @@
 
         it 'returns the original' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -strip #{filename} png:-")
+            .with("convert -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -92,7 +92,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -crop 60x75+80+15 -strip #{filename} png:-")
+            .with("convert -crop 60x75+80+15 -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -102,7 +102,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -crop 80.0%x70.0+18+13 -strip #{filename} png:-")
+            .with("convert -crop 80.0%x70.0+18+13 -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -112,7 +112,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -crop 131x131+22+0 -strip #{filename} png:-")
+            .with("convert -crop 131x131+22+0 -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -134,7 +134,7 @@
 
         it 'returns the original' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -strip #{filename} png:-")
+            .with("convert -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -144,7 +144,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -resize 50.0% -strip #{filename} png:-")
+            .with("convert -resize 50.0% -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -154,7 +154,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -resize 12.5% -strip #{filename} png:-")
+            .with("convert -resize 12.5% -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -164,7 +164,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -resize 50 -strip #{filename} png:-")
+            .with("convert -resize 50 -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -174,7 +174,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -resize x50 -strip #{filename} png:-")
+            .with("convert -resize x50 -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -184,7 +184,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -resize 150x75! -strip #{filename} png:-")
+            .with("convert -resize 150x75! -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -193,7 +193,7 @@
 
         it 'runs the correct imagemagick command' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -resize 150x75 -strip #{filename} png:-")
+            .with("convert -resize 150x75 -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -215,7 +215,7 @@
 
         it 'returns the original' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -strip #{filename} png:-")
+            .with("convert -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -225,7 +225,7 @@
 
         it 'handles floats' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -virtual-pixel white +distort srt 22.5 -strip #{filename} png:-")
+            .with("convert -virtual-pixel white +distort srt 22.5 -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -247,7 +247,7 @@
 
         it 'returns the original when specifing default' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -strip #{filename} png:-")
+            .with("convert -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -257,7 +257,7 @@
 
         it 'returns the original when specifing color' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -strip #{filename} png:-")
+            .with("convert -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -267,7 +267,7 @@
 
         it 'converts to grayscale' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -colorspace Gray -strip #{filename} png:-")
+            .with("convert -colorspace Gray -strip -flatten #{filename} png:-")
           render
         end
       end
@@ -277,7 +277,7 @@
 
         it 'converts to bitonal' do
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with("convert -colorspace Gray -type Bilevel -strip #{filename} png:-")
+            .with("convert -colorspace Gray -type Bilevel -strip -flatten #{filename} png:-")
           render
         end
       end
diff --git a/spec/transformers/riiif/kakadu_transformer_spec.rb b/spec/transformers/riiif/kakadu_transformer_spec.rb
index d2be599..e830ba2 100644
--- a/spec/transformers/riiif/kakadu_transformer_spec.rb
+++ b/spec/transformers/riiif/kakadu_transformer_spec.rb
@@ -42,7 +42,7 @@
           .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 ' \
                 '-region "{0.1,0.2},{0.1,0.1}" -reduce 4 -o /tmp/foo.bmp')
         expect(Riiif::CommandRunner).to receive(:execute)
-          .with('convert -resize 38x38! -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+          .with('convert -resize 38x38! -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
         transform
       end
     end
@@ -54,7 +54,7 @@
           expect(Riiif::CommandRunner).to receive(:execute)
             .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 -o /tmp/foo.bmp')
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with('convert -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+            .with('convert -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
           transform
         end
       end
@@ -67,7 +67,7 @@
           expect(Riiif::CommandRunner).to receive(:execute)
             .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 -o /tmp/foo.bmp')
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with('convert -resize 651 -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+            .with('convert -resize 651 -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
           transform
         end
       end
@@ -80,7 +80,7 @@
           expect(Riiif::CommandRunner).to receive(:execute)
             .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 -o /tmp/foo.bmp')
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with('convert -resize x581 -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+            .with('convert -resize x581 -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
           transform
         end
       end
@@ -96,7 +96,7 @@
           expect(Riiif::CommandRunner).to receive(:execute)
             .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 -reduce 1 -o /tmp/foo.bmp')
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with('convert -resize 60.0% -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+            .with('convert -resize 60.0% -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
           transform
         end
       end
@@ -109,7 +109,7 @@
           expect(Riiif::CommandRunner).to receive(:execute)
             .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 -reduce 1 -o /tmp/foo.bmp')
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with('convert -resize 408 -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+            .with('convert -resize 408 -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
           transform
         end
       end
@@ -122,7 +122,7 @@
           expect(Riiif::CommandRunner).to receive(:execute)
             .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 -reduce 1 -o /tmp/foo.bmp')
           expect(Riiif::CommandRunner).to receive(:execute)
-            .with('convert -resize x481 -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+            .with('convert -resize x481 -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
           transform
         end
       end
@@ -135,7 +135,7 @@
         expect(Riiif::CommandRunner).to receive(:execute)
           .with('kdu_expand -quiet -i baseball.jp2 -num_threads 4 -reduce 2 -o /tmp/foo.bmp')
         expect(Riiif::CommandRunner).to receive(:execute)
-          .with('convert -resize 80.0% -quality 85 -sampling-factor 4:2:0 -strip /tmp/foo.bmp jpg:-')
+          .with('convert -resize 80.0% -quality 85 -sampling-factor 4:2:0 -strip -flatten /tmp/foo.bmp jpg:-')
         transform
       end
     end