diff --git a/data-prepper-plugins/s3-source/src/main/java/org/opensearch/dataprepper/plugins/source/S3InputStream.java b/data-prepper-plugins/s3-source/src/main/java/org/opensearch/dataprepper/plugins/source/S3InputStream.java
index 0629db6831..14f8a509ff 100644
--- a/data-prepper-plugins/s3-source/src/main/java/org/opensearch/dataprepper/plugins/source/S3InputStream.java
+++ b/data-prepper-plugins/s3-source/src/main/java/org/opensearch/dataprepper/plugins/source/S3InputStream.java
@@ -129,11 +129,15 @@ public int read() throws IOException {
         Preconditions.checkState(!closed, "Cannot read: already closed");
         positionStream();
 
-        pos += 1;
-        next += 1;
-        bytesCounter.increment();
+        final int byteRead = stream.read();
 
-        return stream.read();
+        if (byteRead != -1) {
+            pos += 1;
+            next += 1;
+            bytesCounter.increment();
+        }
+
+        return byteRead;
     }
 
     /**
@@ -161,10 +165,13 @@ public int read(byte[] b, int off, int len) throws IOException {
         Preconditions.checkState(!closed, "Cannot read: already closed");
         positionStream();
 
-        int bytesRead = stream.read(b, off, len);
-        pos += bytesRead;
-        next += bytesRead;
-        bytesCounter.add(bytesRead);
+        final int bytesRead = stream.read(b, off, len);
+
+        if (bytesRead > 0) {
+            pos += bytesRead;
+            next += bytesRead;
+            bytesCounter.add(bytesRead);
+        }
 
         return bytesRead;
     }
@@ -203,9 +210,11 @@ public int readNBytes(byte[] b, int off, int len) throws IOException {
 
         final int bytesRead = stream.readNBytes(b, off, len);
 
-        pos += bytesRead;
-        next += bytesRead;
-        bytesCounter.add(bytesRead);
+        if (bytesRead > 0) {
+            pos += bytesRead;
+            next += bytesRead;
+            bytesCounter.add(bytesRead);
+        }
 
         return bytesRead;
     }
@@ -325,9 +334,11 @@ public void readFully(byte[] bytes, int start, int len) throws IOException {
 
         int bytesRead = readFully(stream, bytes, start, len);
 
-        this.pos += bytesRead;
-        this.next += bytesRead;
-        this.bytesCounter.add(bytesRead);
+        if (bytesRead > 0) {
+            this.pos += bytesRead;
+            this.next += bytesRead;
+            this.bytesCounter.add(bytesRead);
+        }
     }
 
     /**
@@ -354,9 +365,11 @@ public int read(ByteBuffer buf) throws IOException {
             bytesRead = readDirectBuffer(stream, buf, temp);
         }
 
-        this.pos += bytesRead;
-        this.next += bytesRead;
-        this.bytesCounter.add(bytesRead);
+        if (bytesRead > 0) {
+            this.pos += bytesRead;
+            this.next += bytesRead;
+            this.bytesCounter.add(bytesRead);
+        }
 
         return bytesRead;
     }
@@ -385,9 +398,11 @@ public void readFully(ByteBuffer buf) throws IOException {
             bytesRead = readFullyDirectBuffer(stream, buf, temp);
         }
 
-        this.pos += bytesRead;
-        this.next += bytesRead;
-        this.bytesCounter.add(bytesRead);
+        if (bytesRead > 0) {
+            this.pos += bytesRead;
+            this.next += bytesRead;
+            this.bytesCounter.add(bytesRead);
+        }
     }
 
     /**
@@ -478,7 +493,7 @@ private void closeStream() throws IOException {
      */
     private void abortStream() {
         try {
-            if (stream instanceof Abortable && stream.read() != -1) {
+            if (stream instanceof Abortable) {
                 ((Abortable) stream).abort();
             }
         } catch (Exception e) {
diff --git a/data-prepper-plugins/s3-source/src/test/java/org/opensearch/dataprepper/plugins/source/S3InputStreamTest.java b/data-prepper-plugins/s3-source/src/test/java/org/opensearch/dataprepper/plugins/source/S3InputStreamTest.java
index 1ac31890ee..d75254189d 100644
--- a/data-prepper-plugins/s3-source/src/test/java/org/opensearch/dataprepper/plugins/source/S3InputStreamTest.java
+++ b/data-prepper-plugins/s3-source/src/test/java/org/opensearch/dataprepper/plugins/source/S3InputStreamTest.java
@@ -15,6 +15,7 @@
 import software.amazon.awssdk.services.s3.model.S3Exception;
 
 import java.io.ByteArrayInputStream;
+import java.io.EOFException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.ByteBuffer;
@@ -103,6 +104,19 @@ void testRead() throws IOException {
         verify(s3ObjectSizeProcessedSummary).record(1.0);
     }
 
+    @Test
+    void testReadEndOfFile() throws IOException {
+        InputStream inputStream = new ByteArrayInputStream("".getBytes());
+        when(s3Client.getObject(any(GetObjectRequest.class), any(ResponseTransformer.class))).thenReturn(inputStream);
+
+        int firstByte = s3InputStream.read();
+        assertEquals(-1, firstByte);
+
+        s3InputStream.close();
+
+        verify(s3ObjectSizeProcessedSummary).record(0.0);
+    }
+
     @Test
     void testReadByteArray() throws IOException {
         InputStream inputStream = new ByteArrayInputStream("Test data".getBytes());
@@ -150,6 +164,20 @@ void testReadNBytes_intoArray() throws Exception {
         verify(s3ObjectSizeProcessedSummary).record(4.0);
     }
 
+    @Test
+    void testReadNBytes_endOfFile() throws Exception {
+        InputStream inputStream = new ByteArrayInputStream("".getBytes());
+        when(s3Client.getObject(any(GetObjectRequest.class), any(ResponseTransformer.class))).thenReturn(inputStream);
+
+        byte[] buffer = new byte[9];
+        int bytesRead = s3InputStream.readNBytes(buffer, 0, 4);
+
+        assertEquals(0, bytesRead);
+
+        s3InputStream.close();
+        verify(s3ObjectSizeProcessedSummary).record(0.0);
+    }
+
     @Test
     void testReadNBytes_getArray() throws Exception {
         InputStream inputStream = new ByteArrayInputStream("Test data".getBytes());
@@ -242,6 +270,19 @@ void testReadFullyByteBuffer() throws IOException {
         verify(s3ObjectSizeProcessedSummary).record(4.0);
     }
 
+    @Test
+    void testReadFullyByteBuffer_endOfFile() throws IOException {
+        InputStream inputStream = new ByteArrayInputStream("".getBytes());
+        when(s3Client.getObject(any(GetObjectRequest.class), any(ResponseTransformer.class))).thenReturn(inputStream);
+        s3InputStream.seek(0); // Force opening the stream
+
+        ByteBuffer buffer = ByteBuffer.allocate(4);
+        assertThrows(EOFException.class, () -> s3InputStream.readFully(buffer));
+
+        s3InputStream.close();
+        verify(s3ObjectSizeProcessedSummary).record(0.0);
+    }
+
     @Test
     void testReadFullyHeapBuffer() throws IOException {
         InputStream inputStream = new ByteArrayInputStream("Test data".getBytes());