Unaware of hostile undercurrents, the Commission started preparing for the elections, scheduled for June 2007. The Bahadur Bhavan faced innumerable hurdles, owing to the post-conflict situation. More importantly, handling the former rebels—who threatened to walk out of the election process whenever they did not get what they wanted— was extremely difficult. For example, during the allocation of party symbols to be used during the elections, the Maoists threatened to walk out if they were not given the hammer and sickle symbol. The Commission could not oblige because the other communist parties objected, saying the hammer and sickle was the symbol of all communist parties. But after a series of negotiations, the Commission found a solution: granting the hammer and sickle to the Maoists—while placating the other parties by placing the common symbol inside a small circle. Despite this creative outcome the EC was criticised for pleasing the Maoists.

In addition to these post-conflict challenges, the Commission faced obstacles, owing to Nepal's geographical diversity and poor infrastructure. In more than half the country, there were no roads and the Commission had to rely on air travel. That too was not easy. In one incident, the helicopter containing training materials could not fly to the mountainous Solukhumbu district for a week, due to bad weather—meaning preparations for the training had to be redone. The biggest difficulty was created by the frequent shortage of petrol, diesel and kerosene. As a result, the Commission had to reschedule crucial trainings and other election preparations in many districts.