By 1809, if the hospital was to survive, the Alamo buildings needed extensive renovation. Three local masons examined the convento structure and made estimates of the necessary repairs, materials, and Cósts. The majority of the flat cement roofs had to be replaced; most of the walls had to be patched, plastered, and whitewashed; many of the floors needed to be rebuilt; and two areas where walls were about to fall had to be reconstructed. Most of the roofing beams and roof drains were rotten and needed to be replaced (Bexar County Archives [BA], Office of the County Clerk, Bexar County Courthouse, San Antonio, Texas, May 2, 1809, microfilm roll 41:205). The work took almost a year to complete and Cóst about 6,000 pesos (Nixon 1936:2728). This was apparently the last major repair and construction on the Alamo buildings until 1835. The hospital was closed around 1812 as the financial and political problems of Spain in Texas increased (Nixon 1936:28).
From 1812 until about 1820, revolution and unrest kept the Compañía Volante away from the Alamo most of the time. During this period the abandoned convento buildings deteriorated, and roofs and walls began to decay and collapse again. By about 1825, soldiers and local citizens began to petition the Mexican government for the right to purchase the Indian quarters and other land belonging to the Alamo outside the convento and church; during the late 1820s, the Mexican government consented (BA March 13, 1829, microfilm roll 120:728).
With the onset of hostilities between Anglo American Texans and the Mexican government in 1835, General Perfecto de Cós, commander of the Mexican forces in Texas, began to fortify San Antonio and the Alamo. Just how much of the fortifications were built by Cós and how much by the Texans later, in 1836, is questionable. Lord (1961:60, 77) presents the view that the majority of the defenses were built by the Texans, but this was probably not the case. According to Samuel Maverick's journal (Green 1952:28), written in San Antonio during most of the siege of Bexar (October-December 1835), Cós arrived in San Antonio on October 8. Texan troops marching on San Antonio from Gonzales began to be reported on October 12; on that date Cós ordered the fortification of the Alamo to begin: "Timbers & c. taken to El Alamo to fortify the Quartel" (Green 1952:29). By October 18, 300 cavalry and 200 infantry were stationed in the Alamo and available to be used as work force. The Texan troops crossed Salado Creek and reached the immediate area of San Antonio on October 21. A series of small actions began between the Mexican and Texan forces, but never escalated into a full-scale battle.
On October 26, 1835, Maverick noted, "an 18 pounder just mounted. Was carried by to the Alamo [sic]n (Green 1952:32). He added this made seven cannons mounted in the Alamo, "of which one, the 18 pounder, is on the top of the old church of San Antonio" (Green 1952:32). By November 3, Maverick stated, "the quartel in the Alamo is very strongly fortified" (Green 1952:35). After that date he made no further references to fortification work at the Alamo. Throughout November 1835, Maverick observed repeated instances of exchanges of cannon, musket, and rifle fire between the Mexican troops within the Alamo and the Texan forces besieging San Antonio. Throughout the fortification and siege, Maverick indicated that Colonel Domingo de Ugartechea was in command of the fortification and defense of the Alamo, while Cós commanded the defenses built around Military Plaza in San Antonio.