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We could therefore use something like the following, to modify the quality of the original jpeg image file to e.g. 90%:

/**
 * A) Modify the quality of original jpeg images to 90%
 */
add_filter( 'wp_handle_upload', function( $data )
{
    if( ! isset( $data['file'] ) || ! isset( $data['type'] ) )
        return $data;

    // Target jpeg images       
    if( in_array( $data['type'], [ 'image/jpg', 'image/jpeg' ] ) )
    {
        // Check for a valid image editor
        $editor = wp_get_image_editor( $data['file'] );    
        if( ! is_wp_error( $editor ) )
        {
            // Set the new image quality
            $result = $editor->set_quality( 90 );

            // Re-save the original image file
            if( ! is_wp_error( $result ) )
                $editor->save( $data['file'] );
        }
    }
    return $data;
} );

If we take a look at the media_handle_upload() function, we might consider hooking into the wp_generate_attachment_metadata filter instead, to modify the original jpeg image file, after the intermediate sizes have been generated.

/**
 * B) Modify the quality of original jpeg images to 90%
 */
add_filter( 'wp_generate_attachment_metadata', function( $metadata, $attachment_id ) 
{
    $file = get_attached_file( $attachment_id );
    $type = get_post_mime_type( $attachment_id );
        
    // Target jpeg images
    if( in_array( $type, [ 'image/jpg', 'image/jpeg' ] ) )
    {
        // Check for a valid image editor
        $editor = wp_get_image_editor( $file );
        if( ! is_wp_error( $editor ) )
        {
            // Set the new image quality
            $result = $editor->set_quality( 90 );

            // Re-save the original image file
            if( ! is_wp_error( $result ) )
                $editor->save( $file );
        }
    }   
    return $metadata;
}, 10, 2 );

Update: Just did some simple testing. Here we can see that when the full size image is re-saved at %1 quality then all the intermediate sizes (300x200 and 150x150) in:

A) We could therefore use something like the following, to modify the quality of the original jpeg image file (to e.g. 90) during uploads:

/**
 * A) Modify the quality of original jpeg images to 90, during uploads
 */
add_filter( 'wp_handle_upload', function( $data )
{
    if( ! isset( $data['file'] ) || ! isset( $data['type'] ) )
        return $data;

    // Target jpeg images       
    if( in_array( $data['type'], [ 'image/jpg', 'image/jpeg' ] ) )
    {
        // Check for a valid image editor
        $editor = wp_get_image_editor( $data['file'] );    
        if( ! is_wp_error( $editor ) )
        {
            // Set the new image quality
            $result = $editor->set_quality( 90 );

            // Re-save the original image file
            if( ! is_wp_error( $result ) )
                $editor->save( $data['file'] );
        }
    }
    return $data;
} );

B) If we take a look at the media_handle_upload() function, we might consider hooking into the wp_generate_attachment_metadata filter instead, to modify the original jpeg image file, after the intermediate sizes have been generated.

/**
 * B) Modify the quality of original jpeg images to 90, during uploads
 */
add_filter( 'wp_generate_attachment_metadata', function( $metadata, $attachment_id ) 
{
    $file = get_attached_file( $attachment_id );
    $type = get_post_mime_type( $attachment_id );
        
    // Target jpeg images
    if( in_array( $type, [ 'image/jpg', 'image/jpeg' ] ) )
    {
        // Check for a valid image editor
        $editor = wp_get_image_editor( $file );
        if( ! is_wp_error( $editor ) )
        {
            // Set the new image quality
            $result = $editor->set_quality( 90 );

            // Re-save the original image file
            if( ! is_wp_error( $result ) )
                $editor->save( $file );
        }
    }   
    return $metadata;
}, 10, 2 );

Update: Just did some simple testing with an image of our kitchen wall clock. Here we can see that when the full size image is re-saved, with quality 5, then all the intermediate sizes:

Here are the combined results:

If we take a look at the media_handle_upload() function, we might consider hooking into the wp_generate_attachment_metadata filter instead, to modify the original jpeg image file, after the intermediate sizes have been generated?

If we take a look at the media_handle_upload() function, we might consider hooking into the wp_generate_attachment_metadata filter instead, to modify the original jpeg image file, after the intermediate sizes have been generated.

/**
 * B) Modify the quality of original jpeg images to 90%
 */
add_filter( 'wp_generate_attachment_metadata', function( $metadata, $attachment_id ) 
{
    $file = get_attached_file( $attachment_id );
    $type = get_post_mime_type( $attachment_id );
        
    // Target jpeg images
    if( in_array( $type, [ 'image/jpg', 'image/jpeg' ] ) )
    {
        // Check for a valid image editor
        $editor = wp_get_image_editor( $file );
        if( ! is_wp_error( $editor ) )
        {
            // Set the new image quality
            $result = $editor->set_quality( 90 );

            // Re-save the original image file
            if( ! is_wp_error( $result ) )
                $editor->save( $data['file'] );
        }
    }   
    return $metadata;
}, 10, 2 );

/**
 * B) Modify the quality of original jpeg images to 90%
 */
add_filter( 'wp_generate_attachment_metadata', function( $metadata, $attachment_id ) 
{
    $file = get_attached_file( $attachment_id );
    $type = get_post_mime_type( $attachment_id );
        
    // Target jpeg images
    if( in_array( $type, [ 'image/jpg', 'image/jpeg' ] ) )
    {
        // Check for a valid image editor
        $editor = wp_get_image_editor( $file );
        if( ! is_wp_error( $editor ) )
        {
            // Set the new image quality
            $result = $editor->set_quality( 90 );

            // Re-save the original image file
            if( ! is_wp_error( $result ) )
                $editor->save( $file );
        }
    }   
    return $metadata;
}, 10, 2 );