diff --git a/src/nvim/input_cmdatom.c b/src/nvim/input_cmdatom.c
index 81b5a700f3..e2ba43dada 100644
--- a/src/nvim/input_cmdatom.c
+++ b/src/nvim/input_cmdatom.c
@@ -194,7 +194,7 @@ CmdSpec atom_cmd_spec(const cmdarg_T *cap)
 static CmdOrigin atom_origin(void)
 {
   CmdOrigin origin = { .win = curwin, .pos = curwin->w_cursor,
-                       .tick = buf_get_changedtick(curbuf) };
+                       .tick = buf_get_changedtick(curbuf), .maptick = maptick };
   set_bufref(&origin.buf, curbuf);
   return origin;
 }
@@ -1167,9 +1167,12 @@ InsSession atom_ins_start(int cmd, long count, VisualIns vis, bool vblock)
 void atom_ins_end(const InsSession *session, bool busy)
 {
   bool visual = session->vis != kVInsNone;
-  if (!session->typed || busy || restart_edit != 0 || !atom_buf_has_consumers()
+  bool user_input = session->typed
+                    // A session is user input, if user input occurred during it. #41516
+                    || maptick != session->origin.maptick;
+  if (!user_input || busy || restart_edit != 0 || !atom_buf_has_consumers()
       || (visual && session->vis != kVInsKeys)) {
-    if (session->typed && (busy || restart_edit != 0) && atom_composite_active()) {
+    if (user_input && (busy || restart_edit != 0) && atom_composite_active()) {
       // Incomplete session (i_CTRL-O): its resolution is never captured.
       composite.lossy = true;
     }
diff --git a/src/nvim/input_cmdatom_defs.h b/src/nvim/input_cmdatom_defs.h
index 6c6940fa7f..7347adaae3 100644
--- a/src/nvim/input_cmdatom_defs.h
+++ b/src/nvim/input_cmdatom_defs.h
@@ -36,6 +36,7 @@ typedef struct {
   const win_T *win;   ///< Window.
   pos_T pos;          ///< Cursor position. Stored here bc the window might be closed.
   varnumber_T tick;   ///< b:changedtick.
+  int maptick;        ///< Advances on typed input (globals.h:maptick).
 } CmdOrigin;
 
 /// How an insert-session was entered from Visual mode.
diff --git a/test/functional/editor/cmdatom_spec.lua b/test/functional/editor/cmdatom_spec.lua
index 16ddad36d5..d33c78571d 100644
--- a/test/functional/editor/cmdatom_spec.lua
+++ b/test/functional/editor/cmdatom_spec.lua
@@ -939,7 +939,7 @@ describe('CmdAtom', function()
     )
   end)
 
-  it('an insert session atom captures its text', function()
+  it('insert-session atom captures its text', function()
     fn.setline(1, { 'aaa' })
     feed('gg0')
     atoms_start()
@@ -966,6 +966,38 @@ describe('CmdAtom', function()
     eq({ type = 'insert', count = 3, text = 'Z' }, pick(atom_last(), 'type', 'count', 'text'))
   end)
 
+  it('insert-session entered programmatically, still captures *user* input #41516', function()
+    atoms_start()
+    n.exec_lua([[
+      vim.keymap.set('i', '<C-j>', function()
+        vim.api.nvim_feedkeys(vim.api.nvim_replace_termcodes('<Esc>', true, false, true), 'n', false)
+        vim.schedule(function()
+          vim.api.nvim_feedkeys('i', 'n', false)
+        end)
+      end)
+    ]])
+    local before = #atoms()
+    feed('i')
+    n.exec_lua('vim.wait(50)')
+    feed('<C-j>')
+    n.exec_lua('vim.wait(50)')
+    feed('<Esc>')
+    local evs = atoms()
+    eq(before + 2, #evs)
+    eq({ k('1i<Esc>'), k('1i<Esc>') }, { evs[#evs - 1].keys, evs[#evs].keys })
+    -- Typed text within such a session lands in its atom...
+    n.exec_lua([[vim.schedule(function() vim.api.nvim_feedkeys('i', 'n', false) end)]])
+    n.exec_lua('vim.wait(50)')
+    feed('hi<Esc>')
+    eq({ text = 'hi', keys = k('1ihi<Esc>') }, pick(atom_last(), 'text', 'keys'))
+    -- ...but with NO typed input within it, the session emits nothing.
+    before = #atoms()
+    n.exec_lua([[vim.schedule(function() vim.api.nvim_feedkeys('i', 'n', false) end)]])
+    n.exec_lua('vim.wait(50)')
+    n.exec_lua([[vim.api.nvim_feedkeys('\27', 'n', false)]])
+    eq(before, #atoms())
+  end)
+
   it("operatorfunc atom includes the getchar()'d payload", function()
     n.exec(t_atom.minisurround_vim)
     fn.setline(1, { 'alpha beta' })