Between 1823 and 1824, Baquedano participated in the Peruvian War of Independence and later under General Ramón Freire in the capture of Chiloé (1826) and all the campaigns between 1827 and 1829. During the Chilean Civil War of 1829 he served under the banners of General José Joaquín Prieto, and fought at the battles of Ochagavía (1829) and Lircay (1830). During the War of the Confederation, he fought under Manuel Bulnes at the battles of Portada de Guías (1838) and Yungay (1839) where he was injured and promoted to Brigadier General.