Manuel Santa Cruz Loidi was descendant to Basque rural working-class families; generations of his ancestors were farmers living in the Oria river valley, in the Gipuzkoan county of Tolosa.
His paternal grandfather Pascual de Santa Cruz was a native of Andoain yet he settled in Elduain, probably on the economy of his wife María Bautista Sarove.
Their son and the father of Manuel Ignacio, Francisco Antonio Santa Cruz Sarove (1784-1842), in 1824 married Juana Josefa Loidi Urrestarazu (1803–1871); she was the daughter of Miguel Ignacio Loidi, a native of Amezketa, and María Ignacia Urrestarazu, who originated from Orendain.
The couple lived in Elduain; their caserio, known as Zamonea, was among the poorer ones in the village.
It is not clear how many children they had, though according to some sources Manuel Ignacio was not their only child and he had at least one sister.
Following the death of her husband María Ignacia remarried with a widower Juan Ignacio Betelu Muñagorri (1795–1861); it is not clear whether they had any offspring.

Manuel was raised by his mother and step-father and initially did not differ from other village boys.
It is not clear where he was first educated; at some stage he was taken care of by his much older paternal cousin, a local priest Francisco Antonio Sasiain Santa Cruz (1812–1898); he taught the teenager Latin and apparently directed him towards the religious career.
Indeed, in 1861 Manuel entered the seminary in Vitoria; during the first 3 years he was obtaining high grades and was rewarded with the meritissimus title; later his performance worsened, reportedly due to health problems.
He was ordained as a priest in 1866 and posted to Hernialde, a village a few miles from his native one.
According to some sources he was first nominated a coadjutor; other authors claim he initially acted as a vicar.
Following the death of the parish priest it was Santa Cruz who became his successor at an unspecified time in the late 1860s; he allegedly assumed his duties with frenetic energy and as a spiritual shepherd he tended to rigidity, himself adhering to an austere living pattern.

Since his father had served as a Carlist volunteer during the last civil war and since legitimist sympathies prevailed among the rural Gipuzkoan folk, it is likely that Manuel from his youth was growing in an ambience strongly flavored with Carlism.
His position was probably strengthened during the seminary years, as Carlism was popular also among the lower and regular clergy of the province.
In line with the Traditionalist outlook Santa Cruz assumed a decisively hostile stand towards the 1868 revolution, from behind the pulpit lambasting the new regime as an ungodly, depraved system.
His inflammatory sermons gained him attention of the authorities; in October 1870 a Guardia Civil patrol showed up in Hernialde to detain him after a Sunday Mass. Santa Cruz took advantage of a somewhat loose approach of his captors and fled, in a few days crossing to France.
Manuel Santa Cruz Loidi was descendant to Basque rural working-class families; generations of his ancestors were farmers living in the Oria river valley, in the Gipuzkoan county of Tolosa. His paternal grandfather Pascual de Santa Cruz was a native of Andoain yet he settled in Elduain, probably on the economy of his wife María Bautista Sarove. Their son and the father of Manuel Ignacio, Francisco Antonio Santa Cruz Sarove (1784-1842), in 1824 married Juana Josefa Loidi Urrestarazu (1803–1871); she was the daughter of Miguel Ignacio Loidi, a native of Amezketa, and María Ignacia Urrestarazu, who originated from Orendain. The couple lived in Elduain; their caserio, known as Zamonea, was among the poorer ones in the village. It is not clear how many children they had, though according to some sources Manuel Ignacio was not their only child and he had at least one sister. Following the death of her husband María Ignacia remarried with a widower Juan Ignacio Betelu Muñagorri (1795–1861); it is not clear whether they had any offspring.
Manuel was raised by his mother and step-father and initially did not differ from other village boys. It is not clear where he was first educated; at some stage he was taken care of by his much older paternal cousin, a local priest Francisco Antonio Sasiain Santa Cruz (1812–1898); he taught the teenager Latin and apparently directed him towards the religious career. Indeed, in 1861 Manuel entered the seminary in Vitoria; during the first 3 years he was obtaining high grades and was rewarded with the meritissimus title; later his performance worsened, reportedly due to health problems. He was ordained as a priest in 1866 and posted to Hernialde, a village a few miles from his native one. According to some sources he was first nominated a coadjutor; other authors claim he initially acted as a vicar. Following the death of the parish priest it was Santa Cruz who became his successor at an unspecified time in the late 1860s; he allegedly assumed his duties with frenetic energy and as a spiritual shepherd he tended to rigidity, himself adhering to an austere living pattern. 
Since his father had served as a Carlist volunteer during the last civil war and since legitimist sympathies prevailed among the rural Gipuzkoan folk, it is likely that Manuel from his youth was growing in an ambience strongly flavored with Carlism. His position was probably strengthened during the seminary years, as Carlism was popular also among the lower and regular clergy of the province. In line with the Traditionalist outlook Santa Cruz assumed a decisively hostile stand towards the 1868 revolution, from behind the pulpit lambasting the new regime as an ungodly, depraved system. His inflammatory sermons gained him attention of the authorities; in October 1870 a Guardia Civil patrol showed up in Hernialde to detain him after a Sunday Mass. Santa Cruz took advantage of a somewhat loose approach of his captors and fled, in a few days crossing to France.
Manuel Santa Cruz Loidi