On 16 October 2005, he was "badly beaten by unidentified armed men", which Amnesty International interpreted to be a result of his criticisms of the electoral procedures.

[7][1] In December 2007, he and Netsanet Demissie were convicted in the Ethiopian Federal High Court for "provoking and preparing 'outrages against the Constitution'" but acquitted of committing "outrages", by a majority of two judges out of three, after a two-year trial.

Amnesty International considered Daniel's and Netsanet's detention and conviction to have been only based on their human rights activities, and defined both as having been prisoners of conscience.

[1][2] Amnesty director for Africa, Erwin van der Borght, stated, "It is deplorable that civil society activists who are prisoners of conscience like Daniel Bekele and Netsanet Demissie can be arrested and unfairly convicted simply for peacefully conducting human rights work.

[6] In September 2021, Daniel was awarded the 2021 German Africa Prize for his commitment to defending human rights and democracy.