Following some 18 months of exile in Bayonne, in 1872–73 Santa Cruz was taking part in the guerilla warfare prior and during the Third Carlist War.
His record falls into 4 separate strings: from April till May 1872, from June till August 1872, from December 1872 till July 1873, and in December 1873, all separated by periods of taking refuge in France.
Initially, he joined a unit led by a Carlist veteran Pedro Recondo; serving as a chaplain, Santa Cruz was gaining experience in rural irregular tactics.
Since the summer of 1872 he was leading his own troops; initially the group consisted of some 15–25 men, but later it grew and in literature is estimated at 200, 500, or even 1,000, with an informal, in-between command structure built up.
The detachment was rather loosely incorporated into the Carlist war effort; at early stages it was assigned a vague task of "guarding the Northern borderline" by the legitimist general staff, yet it seems that the unit retained great autonomy and operated independently.

In military terms the activity of Santa Cruz’ unit consisted of harassing the enemy logistics network and raiding minor garrisons.
The former included disrupting postal service, arms transports, or railway connections; the latter included descending upon smaller locations and destroying archives, pillaging Guardia Civil or Carabineros posts, abducting local officials, and staging shows of prowess.
The Liberal high command was forced to diminish their frontline strength and to assign more troops to vigilance and patrol duties.
However, in line with his guerilla strategy Santa Cruz avoided open confrontation against enemy forces; cases of accepting a battle usually resulted in defeat, e.g. in Aia.
When facing enemy roundup Santa Cruz used to disband his group and to set re-assembly terms; taking advantage of perfect familiarity with the mountainous Gipuzkoan countryside and support of the local population, he kept evading the governmental chase.
Santa Cruz operated across all the province of Gipuzkoa, though he was noted also in neighboring areas of Biscay, Álava, and particularly Navarre.

Since early 1873 Santa Cruz gained notoriety for cruelty and was charged with committing acts of barbarity.
They consisted of executions of prisoners, including women or members of his own unit when suspected of treason, burning down settlements, or administering corporal punishment.
The episode which caused particular outrage occurred in June 1873, when santacrucistas assaulted a fortified provincial border control post in Endarlaza.
Claiming that during the shootout the defenders had mischievously displayed a white flag to fire at the approaching Carlists later on, Santa Cruz had his men execute 35 carabineros who had ultimately surrendered.
The Carlist high command was continuously uneasy about Santa Cruz; the Enderlaza episode proved to be the last straw.
The local legitimist commander general Antonio Lizarraga, who was trying to bring Santa Cruz in line for some time, demanded that the insubordinate priest back down.
Eventually, Santa Cruz found himself hunted down by the Liberals and the Carlists alike; he disbanded his unit and withdrew into France.
Following some 18 months of exile in Bayonne, in 1872–73 Santa Cruz was taking part in the guerilla warfare prior and during the Third Carlist War. His record falls into 4 separate strings: from April till May 1872, from June till August 1872, from December 1872 till July 1873, and in December 1873, all separated by periods of taking refuge in France. Initially, he joined a unit led by a Carlist veteran Pedro Recondo; serving as a chaplain, Santa Cruz was gaining experience in rural irregular tactics. Since the summer of 1872 he was leading his own troops; initially the group consisted of some 15–25 men, but later it grew and in literature is estimated at 200, 500, or even 1,000, with an informal, in-between command structure built up. The detachment was rather loosely incorporated into the Carlist war effort; at early stages it was assigned a vague task of "guarding the Northern borderline" by the legitimist general staff, yet it seems that the unit retained great autonomy and operated independently.
In military terms the activity of Santa Cruz’ unit consisted of harassing the enemy logistics network and raiding minor garrisons. The former included disrupting postal service, arms transports, or railway connections; the latter included descending upon smaller locations and destroying archives, pillaging Guardia Civil or Carabineros posts, abducting local officials, and staging shows of prowess. The Liberal high command was forced to diminish their frontline strength and to assign more troops to vigilance and patrol duties. However, in line with his guerilla strategy Santa Cruz avoided open confrontation against enemy forces; cases of accepting a battle usually resulted in defeat, e.g. in Aia. When facing enemy roundup Santa Cruz used to disband his group and to set re-assembly terms; taking advantage of perfect familiarity with the mountainous Gipuzkoan countryside and support of the local population, he kept evading the governmental chase. Santa Cruz operated across all the province of Gipuzkoa, though he was noted also in neighboring areas of Biscay, Álava, and particularly Navarre.
Since early 1873 Santa Cruz gained notoriety for cruelty and was charged with committing acts of barbarity. They consisted of executions of prisoners, including women or members of his own unit when suspected of treason, burning down settlements, or administering corporal punishment. The episode which caused particular outrage occurred in June 1873, when santacrucistas assaulted a fortified provincial border control post in Endarlaza. Claiming that during the shootout the defenders had mischievously displayed a white flag to fire at the approaching Carlists later on, Santa Cruz had his men execute 35 carabineros who had ultimately surrendered. The Carlist high command was continuously uneasy about Santa Cruz; the Enderlaza episode proved to be the last straw. The local legitimist commander general Antonio Lizarraga, who was trying to bring Santa Cruz in line for some time, demanded that the insubordinate priest back down. Eventually, Santa Cruz found himself hunted down by the Liberals and the Carlists alike; he disbanded his unit and withdrew into France.
Manuel Santa Cruz Loidi