The human rights charity chief said the rushed drive into promoting a 'Global Britain' has seen Britain strengthen ties with countries which have an abysmal human rights record.
She pointed to recent Government attempts to court diplomats from Saudi Arabia, China and Philippines.
Ms Allen warned that Britain's global reputation could be dragged in the mud after leaving the European Union.
Amnesty warn post-Brexit 'Global Britain' against cosying up to dictators around the world
In an interview with BBC's Today programme, Ms Allen said human rights must determine who Britain makes a deal with, even if it means we lose out on investment and jobs.
Her remarks come as International Trade Secretary Liam Fox was ridiculed for claiming Britain and the Philippines had "shared values" ahead of a meeting with President Duterte.
President Duterte has been accused of leading a violent anti-drug campaign that has killed 7,000 civilians throughout the country in the past year.
She also mentioned recent trade visits to Saudi Arabia, which has been accused of war crimes in its Yemen bombing campaign, as well as a charm offensive to China.
Ms Allen said: "I think there is a moment with trade deals being negotiated to decide what sort of Britain we want to be.
"When we think about the post-Brexit UK and the values we export, people in this country must be shocked to hear that comparison of shared values.
"And then, instead of confronting Saudi Arabia about bombing civilians in Yemen, our Prime Minister sold them £3.3billion worth of arms."
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Protests in Yemen against the Saudi bombing campaign
Amnesty has criticised Rodrigo Duertete for his bloody crackdown
People in this country must be shocked to hear that comparison of shared values
Kate Allen, Amnesty International director
But, Lord Marland, the former trade envoy for David Cameron, said groups like Amnesty were "throwing stones in a glass greenhouse".
He added that unlike many European countries, Britain had set its own rules for conducting trade deals.
Lord Marland cited the Bribery Act, which bans the UK from trading with corrupt countries.
Following Liam Fox's visit to the Phillipines, rival MPs warned the Government against forming friendships with “sinister” leaders.
Labour’s shadow trade secretary Barry Gardiner said: "I’m sorry, but we do not have these shared common values with President Duterte who wants to bring back the death penalty and lower the age of criminal responsibility to nine."
Harriet Harman, chairwoman of Parliament’s committee on human rights, added: "There is a real danger that in our desperation to conclude trade deals respect for human rights, which is in every EU contract, will just go out of the window. "
Amnesty warned Britain's global reputation could be dragged in the mud after Brexit
7,000 people have died during the anti-drug crack down in Philippines
Liberal Democrat foreign affairs spokesman Tom Brake said: "Duterte is one of the 21st century’s most sinister leaders and Liam Fox has flown halfway around the world to grovel to him."
However, a Department of International Trade spokesman said closer ties would help Britain to address areas of concern.