diff --git a/command.c b/command.c
index 6b9301f9d3..87e99f3a92 100644
--- a/command.c
+++ b/command.c
@@ -229,7 +229,7 @@ static bool cmd_set_shader(const char *arg)
    msg_queue_push(g_extern.msg_queue, msg, 1, 120);
    RARCH_LOG("Applying shader \"%s\".\n", arg);
 
-   return video_set_shader_func(type, arg, (1ULL << RARCH_SHADER_MULTIPASS));
+   return video_set_shader_func(type, arg, RARCH_SHADER_INDEX_MULTIPASS);
 }
 
 static const struct cmd_action_map action_map[] = {
diff --git a/driver.h b/driver.h
index 81b93732a8..363d08e694 100644
--- a/driver.h
+++ b/driver.h
@@ -136,13 +136,11 @@ enum rarch_shader_type
    RARCH_SHADER_NONE
 };
 
-enum rarch_shader_mask
+enum rarch_shader_index
 {
-   RARCH_SHADER_MULTIPASS   = 1,
-   RARCH_SHADER_PASS0,
-   RARCH_SHADER_PASS0_STOCK,
-   RARCH_SHADER_PASS1,
-   RARCH_SHADER_PASS1_STOCK
+   RARCH_SHADER_INDEX_MULTIPASS = 0,
+   RARCH_SHADER_INDEX_PASS0 = 1,
+   RARCH_SHADER_INDEX_PASS1 = 2
 };
 
 typedef struct video_info
@@ -233,7 +231,7 @@ typedef struct video_driver
    // Is the window still active?
    bool (*alive)(void *data);
    bool (*focus)(void *data); // Does the window have focus?
-   bool (*set_shader)(void *data, enum rarch_shader_type type, const char *path, unsigned mask); // Sets shader. Might not be implemented.
+   bool (*set_shader)(void *data, enum rarch_shader_type type, const char *path, unsigned index); // Sets shader. Might not be implemented.
    void (*free)(void *data);
    const char *ident;
 
diff --git a/gfx/gl.c b/gfx/gl.c
index ab2fa2bdc7..ad0290c2bf 100644
--- a/gfx/gl.c
+++ b/gfx/gl.c
@@ -1709,75 +1709,73 @@ static bool gl_focus(void *data)
 }
 
 #if defined(HAVE_GLSL) || defined(HAVE_CG)
-static bool gl_set_shader(void *data, enum rarch_shader_type type, const char *path, unsigned mask)
+static bool gl_set_shader(void *data, enum rarch_shader_type type, const char *path, unsigned index)
 {
    gl_t *gl = (gl_t*)data;
 
-   if (mask & (1ULL << RARCH_SHADER_MULTIPASS))
+   if (type == RARCH_SHADER_NONE)
+      return false;
+
+   if (index == RARCH_SHADER_INDEX_MULTIPASS && !path)
    {
+      RARCH_ERR("[GL]: Cannot set stock shader to multipass.\n");
+      return false;
+   }
+
+   if (!gl->shader && index != RARCH_SHADER_INDEX_MULTIPASS)
+   {
+      RARCH_ERR("[GL]: No shader core is init. Cannot set shader %s to pass %u.\n", path, index);
+      return false;
+   }
+
+   if (gl->shader && gl->shader->type != type)
+   {
+      RARCH_ERR("[GL]: Trying to set a specific shader pass %u, but that particular shader core is not initialized.\n", index);
+      return false;
+   }
+
+   // Need full teardown for multipass.
+   if (index == RARCH_SHADER_INDEX_MULTIPASS)
+   {
+      gl_shader_deinit(gl);
+
+      switch (type)
+      {
+#ifdef HAVE_GLSL
+         case RARCH_SHADER_GLSL:
+            gl->shader = &gl_glsl_backend;
+            break;
+#endif
+#ifdef HAVE_CG
+         case RARCH_SHADER_CG:
+            gl->shader = &gl_cg_backend;
+            break;
+#endif
+
+         default:
+            gl->shader = NULL;
+            break;
+      }
+
+      if (!gl->shader)
+      {
+         RARCH_ERR("[GL]: Cannot find shader core for path: %s.\n", path);
+         return false;
+      }
+
 #ifdef HAVE_FBO
       gl_deinit_fbo(gl);
       glBindTexture(GL_TEXTURE_2D, gl->texture[gl->tex_index]);
 #endif
 
-      gl_shader_deinit(gl);
-   }
+      bool ret = gl->shader->init(path);
+      if (!ret)
+      {
+         gl->shader = NULL;
+         RARCH_WARN("[GL]: Failed to set multipass shader. Falling back to stock.\n");
+         return gl->shader->init(NULL);
+      }
 
-   switch (type)
-   {
-#ifdef HAVE_GLSL
-      case RARCH_SHADER_GLSL:
-         if (mask & (1ULL << RARCH_SHADER_MULTIPASS))
-         {
-            if (!gl_glsl_init(path))
-               return false;
-         }
-         else if (mask & (1ULL << RARCH_SHADER_PASS0))
-         {
-#if 0
-            /* TODO - doesn't seem to be added yet? */
-            if (!gl_glsl_load_shader(1, (mask & (1ULL << RARCH_SHADER_PASS0_STOCK)) ? NULL : path))
-#endif
-               return false;
-         }
-         else if (mask & (1ULL << RARCH_SHADER_PASS1))
-         {
-#if 0
-            /* TODO - doesn't seem to be added yet? */
-            if (!gl_glsl_load_shader(2, (mask & (1ULL << RARCH_SHADER_PASS1_STOCK)) ? NULL : path))
-#endif
-               return false;
-         }
-         break;
-#endif
-
-#ifdef HAVE_CG
-      case RARCH_SHADER_CG:
-         if (mask & (1ULL << RARCH_SHADER_MULTIPASS))
-         {
-            if (!gl_cg_init(path))
-               return false;
-         }
-         else if (mask & (1ULL << RARCH_SHADER_PASS0))
-         {
-            if (!gl_cg_load_shader(1, (mask & (1ULL << RARCH_SHADER_PASS0_STOCK)) ? NULL : path))
-               return false;
-         }
-         else if (mask & (1ULL << RARCH_SHADER_PASS1))
-         {
-            if (!gl_cg_load_shader(2, (mask & (1ULL << RARCH_SHADER_PASS1_STOCK)) ? NULL : path))
-               return false;
-         }
-         break;
-#endif
-
-      default:
-         RARCH_ERR("Invalid shader type in gl_set_shader().\n");
-         return false;
-   }
-
-   if (mask & (1ULL << RARCH_SHADER_MULTIPASS))
-   {
 #ifdef HAVE_FBO
       // Set up render to texture again.
       gl_init_fbo(gl, gl->tex_w, gl->tex_h);
@@ -1786,9 +1784,19 @@ static bool gl_set_shader(void *data, enum rarch_shader_type type, const char *p
       // Apparently need to set viewport for passes when we aren't using FBOs.
       gl_set_shader_viewport(gl, 0);
       gl_set_shader_viewport(gl, 1);
+      return true;
    }
+   else // Replace a currently loaded shader directly.
+   {
+      if (index > gl->shader->num_shaders())
+      {
+         RARCH_ERR("Can only load shader for passes that already exist. "
+                  "Attempted to set pass %u, but only %u passes exist.\n", index, gl->shader->num_shaders());
+         return false;
+      }
 
-   return true;
+      return gl->shader->load_shader(index, path);
+   }
 }
 #endif
 
diff --git a/gfx/shader_cg.c b/gfx/shader_cg.c
index a80c1adec2..1a482eae9a 100644
--- a/gfx/shader_cg.c
+++ b/gfx/shader_cg.c
@@ -477,21 +477,30 @@ static bool load_plain(const char *path)
    if (!load_stock())
       return false;
 
-   RARCH_LOG("Loading Cg file: %s\n", path);
-
-   if (!load_program(1, path, true))
-      return false;
-
-   if (*g_settings.video.second_pass_shader && g_settings.video.render_to_texture)
+   if (path)
    {
-      if (!load_program(2, g_settings.video.second_pass_shader, true))
+      RARCH_LOG("Loading Cg file: %s\n", path);
+
+      if (!load_program(1, path, true))
          return false;
 
-      cg_shader_num = 2;
+      if (*g_settings.video.second_pass_shader && g_settings.video.render_to_texture)
+      {
+         if (!load_program(2, g_settings.video.second_pass_shader, true))
+            return false;
+
+         cg_shader_num = 2;
+      }
+      else
+      {
+         prg[2] = prg[0];
+         cg_shader_num = 1;
+      }
    }
    else
    {
-      prg[2] = prg[0];
+      RARCH_LOG("Loading stock Cg file.\n");
+      prg[2] = prg[1] = prg[0];
       cg_shader_num = 1;
    }
 
@@ -1360,5 +1369,8 @@ const gl_shader_backend_t gl_cg_backend = {
    gl_cg_shader_scale,
    gl_cg_set_coords,
    gl_cg_set_mvp,
+
+   gl_cg_load_shader,
+   RARCH_SHADER_CG,
 };
 
diff --git a/gfx/shader_common.h b/gfx/shader_common.h
index 9e30584d3f..582f84ac2f 100644
--- a/gfx/shader_common.h
+++ b/gfx/shader_common.h
@@ -39,6 +39,9 @@ struct gl_shader_backend
    void (*shader_scale)(unsigned index, struct gl_fbo_scale *scale);
    bool (*set_coords)(const struct gl_coords *coords);
    bool (*set_mvp)(const math_matrix *mat);
+
+   bool (*load_shader)(unsigned index, const char *path);
+   enum rarch_shader_type type;
 };
 
 #endif
diff --git a/gfx/shader_glsl.c b/gfx/shader_glsl.c
index 654d593cce..4de50804a2 100644
--- a/gfx/shader_glsl.c
+++ b/gfx/shader_glsl.c
@@ -894,6 +894,8 @@ static bool link_program(GLuint prog)
 
 static bool compile_programs(GLuint *gl_prog, struct shader_program *progs, size_t num)
 {
+   bool ret = true;
+
    for (unsigned i = 0; i < num; i++)
    {
       gl_prog[i] = pglCreateProgram();
@@ -901,7 +903,8 @@ static bool compile_programs(GLuint *gl_prog, struct shader_program *progs, size
       if (gl_prog[i] == 0)
       {
          RARCH_ERR("Failed to create GL program #%u.\n", i);
-         return false;
+         ret = false;
+         goto end;
       }
 
       if (progs[i].vertex)
@@ -911,11 +914,11 @@ static bool compile_programs(GLuint *gl_prog, struct shader_program *progs, size
          if (!compile_shader(shader, progs[i].vertex))
          {
             RARCH_ERR("Failed to compile vertex shader #%u\n", i);
-            return false;
+            ret = false;
+            goto end;
          }
 
          pglAttachShader(gl_prog[i], shader);
-         free(progs[i].vertex);
       }
 
       if (progs[i].fragment)
@@ -925,11 +928,11 @@ static bool compile_programs(GLuint *gl_prog, struct shader_program *progs, size
          if (!compile_shader(shader, progs[i].fragment))
          {
             RARCH_ERR("Failed to compile fragment shader #%u\n", i);
-            return false;
+            ret = false;
+            goto end;
          }
 
          pglAttachShader(gl_prog[i], shader);
-         free(progs[i].fragment);
       }
 
       if (progs[i].vertex || progs[i].fragment)
@@ -938,7 +941,8 @@ static bool compile_programs(GLuint *gl_prog, struct shader_program *progs, size
          if (!link_program(gl_prog[i]))
          {
             RARCH_ERR("Failed to link program #%u\n", i);
-            return false;
+            ret = false;
+            goto end;
          }
 
          GLint location = pglGetUniformLocation(gl_prog[i], "rubyTexture");
@@ -947,7 +951,16 @@ static bool compile_programs(GLuint *gl_prog, struct shader_program *progs, size
       }
    }
 
-   return true;
+end:
+   for (unsigned i = 0; i < num; i++)
+   {
+      free(progs[i].vertex);
+      free(progs[i].fragment);
+      progs[i].vertex   = NULL;
+      progs[i].fragment = NULL;
+   }
+
+   return ret;
 }
 
 static void gl_glsl_reset_attrib(void)
@@ -1014,6 +1027,56 @@ static void find_uniforms(GLuint prog, struct shader_uniforms *uni)
    pglUseProgram(0);
 }
 
+static void gl_glsl_delete_shader(GLuint prog)
+{
+   GLsizei count;
+   GLuint shaders[2] = {0};
+
+   pglGetAttachedShaders(prog, 2, &count, shaders);
+   for (GLsizei i = 0; i < count; i++)
+   {
+      pglDetachShader(prog, shaders[i]);
+      pglDeleteShader(shaders[i]);
+   }
+
+   pglDeleteProgram(prog);
+}
+
+static bool gl_glsl_load_shader(unsigned index, const char *path)
+{
+   pglUseProgram(0);
+
+   if (gl_program[index] != gl_program[0])
+   {
+      gl_glsl_delete_shader(gl_program[index]);
+      gl_program[index] = 0;
+   }
+
+   if (path)
+   {
+      struct shader_program prog = {0};
+      unsigned progs = get_xml_shaders(path, &prog, 1);
+      if (progs != 1)
+         return false;
+
+      if (!compile_programs(&gl_program[index], &prog, 1))
+      {
+         RARCH_ERR("Failed to compile shader: %s.\n", path);
+         return false;
+      }
+
+      find_uniforms(gl_program[index], &gl_uniforms[index]);
+   }
+   else
+   {
+      gl_program[index]  = gl_program[0];
+      gl_uniforms[index] = gl_uniforms[0];
+   }
+
+   pglUseProgram(gl_program[active_index]);
+   return true;
+}
+
 // Platforms with broken get_proc_address.
 // Assume functions are available without proc_address.
 #undef LOAD_GL_SYM
@@ -1129,7 +1192,12 @@ bool gl_glsl_init(const char *path)
       unsigned secondary_progs = get_xml_shaders(g_settings.video.second_pass_shader, progs, 1);
       if (secondary_progs == 1)
       {
-         compile_programs(&gl_program[2], progs, 1);
+         if (!compile_programs(&gl_program[2], progs, 1))
+         {
+            RARCH_ERR("Failed to compile second pass shader.\n");
+            return false;
+         }
+
          num_progs++;
       }
       else
@@ -1185,17 +1253,7 @@ void gl_glsl_deinit(void)
          if (gl_program[i] == 0 || (i && gl_program[i] == gl_program[0]))
             continue;
 
-         GLsizei count;
-         GLuint shaders[2];
-
-         pglGetAttachedShaders(gl_program[i], 2, &count, shaders);
-         for (GLsizei j = 0; j < count; j++)
-         {
-            pglDetachShader(gl_program[i], shaders[j]);
-            pglDeleteShader(shaders[j]);
-         }
-
-         pglDeleteProgram(gl_program[i]);
+         gl_glsl_delete_shader(gl_program[i]);
       }
 
       glDeleteTextures(gl_teximage_cnt, gl_teximage);
@@ -1507,5 +1565,8 @@ const gl_shader_backend_t gl_glsl_backend = {
    gl_glsl_shader_scale,
    gl_glsl_set_coords,
    gl_glsl_set_mvp,
+
+   gl_glsl_load_shader,
+   RARCH_SHADER_GLSL,
 };
 
diff --git a/retroarch.c b/retroarch.c
index 42b983dbed..57057e15e4 100644
--- a/retroarch.c
+++ b/retroarch.c
@@ -2342,7 +2342,7 @@ static void check_shader_dir(void)
       msg_queue_push(g_extern.msg_queue, msg, 1, 120);
       RARCH_LOG("Applying shader \"%s\".\n", shader);
 
-      if (!video_set_shader_func(type, shader, (1ULL << RARCH_SHADER_MULTIPASS)))
+      if (!video_set_shader_func(type, shader, RARCH_SHADER_INDEX_MULTIPASS))
          RARCH_WARN("Failed to apply shader.\n");
    }