Benjamin Saldaña Rocca included Loayza in his original criminal petition against eighteen members of the company for atrocious crimes.

Judge Carlos A. Válcarcel and Walter Ernest Hardenburg implicated Loayza with an incident in 1907 that result in the massacre of multiple Colombians.

[3] The migration further hurt the indigenous of the Putumayo, with many dying from disease while the survivors continued to be exploited for Miguel's financial gain.

[8] Miguel was listed in a document that dated between 1903 and 1906 by Eugene Robuchon as an employee at a substation of El Encanto named La Florida.

[19] This event caught the attention of the Colombian government, who sent Jesús Orjuela, a police inspector to the region to investigate:[21] and set up a meeting with Loayza at El Dorado.

It was a pitiful sight to see these poor Indians, practically naked, their bones almost protruding through their skins, and all branded with the infamous marca de Arana, staggering up the steep hill, carrying upon their doubled backs enormous weights of merchandise for the consumption of their miserable oppressors.

"Hardenburg wrote about his experiences in the Putumayo a few years after he left the region, primarily referring to his time on the Liberal and at El Encanto.

[37] Hardenburg noted: "This band of unfortunates was composed of some thirteen young girls...too young to be called women—were the helpless victims of Loayza and the other chief officials of the Peruvian Amazon Company's El Encanto branch, who violated these tender children without the slightest compunction, and when they tired of them either murdered them or flogged them and sent them back to their tribes.

"These poor wretches, without remedies, without food, were exposed to the burning rays of the vertical sun and the cold rains and heavy dews of early morning until death released them from their sufferings."

[38] Hardenburg's book was greatly benefited from the work of Benjamin Saldaña Rocca, who was a journalist that helped expose the company's actions.

He implicated Loayza and the other employees as perpetrators of the following crimes: fraud, robbery, arson, rape, aggravated homicide, torturing by fire, water, whips, and mutilations.

"[45] The Putumayo genocide devasted the local indigenous populations, whose labor was the real source of profit for the Peruvian Amazon Company.

Miguel Loayza had been active in the Putumayo region since the earliest stages of the genocide, working with Julio César Arana as early as 1901 and dealing in rubber since the late 1880s.

New orders were given by Tizon and Loayza to ensure that each tribe had plantations for food[47] which the extractive operation did not allow them to cultivate prior to liquidation.

[48] Charles Roberts inquired about a letter dated June 10, 1909 from Miguel Loayza, and read its contents out loud to Julio Cesar Arana.

[49] In an English parliament session, Neil Malcolm inquired if Loayza was present at the La Reserva raid, and if his arrest would be pursued.

Sir Edward Grey confirmed that was the same Loayza, however stated the English government had no present grounds to pursue an arrest.

The judge conducted criminal proceedings at several of the plantations that delivered to El Encanto and Loayza, notably the Argelia and La Florida stations.

Valcárcel published a book with his research a year later, in it he stated "Loayza is very cautious, and has always tried not to leave traces of his participation in the crimes of the Putumayo, taking meticulous precautions for that purpose.

"[51] Valcárcel cited written letters and first hand accounts detailing activities around El Encanto to disprove Miguel's innocence.

One statement collected by Valcárcel from Victor Macedo, placed Loyaza at the September 24, 1903 massacre of 25 Ocaina natives, which happened at La Chorrera.

[52] One letter came from a Peruvian military captain, and according to Valcárcel its contents left no doubt to the participation of Loayza in the 1907 incident with the Colombians.

After the scandal of the Putumayo genocide and the liquidation of the company, the Loayza brothers remained administrators at El Encanto, presiding over a native work force.

[56] Before the border change and transition of the Putumayo from Peru to Colombia occurred: Miguel and his brother Carlos organized a series of forced migrations.

The conflict between Colombia and Peru was financially disastrous for the Loayzas who had to abandon some property and make new investments towards the migrations and workforce.

[57] At least 6,719 natives from the Huitoto, Bora, Andoque, and Ocaina populations were forced to relocate deeper into Peru so the Loayzas could retain their workforce.

Settling in the Ampiyacu basin of Loreto, where the Loayzas owned an official land concession, they used the natives to build a 'fundo' enterprise.

The native groups were divided and spread throughout the basin, the Ocaina at Puerto Izango, the Huitoto with Carlos Loayza at Pucaurquillo, among other places.

[59][60] The explorer Romain Wilhelmsen and convicted Nazi war criminal Hermann Becker-Freyseng met Loayza in the mid 1950s.

Romain found out that Loayza was still active in the exploitation of rubber, noting: "huge balls of dark gray latex were piled up beneath his veranda ready for shipment.