What is the right way to close a Panama company?

Dissolve it formally rather than stop paying. A company that stops paying the franchise tax builds up surcharges and fines and is eventually suspended, and that record can follow its owners in later bank checks. Bring the tasa única up to date, then register the dissolution through the resident agent.

Close a company properly

Source: Tasa Única, Dirección General de Ingresos, Ministerio de Economía y Finanzas, Panamá