Border crossings: Peru - Ecuador

Loja - Macara - Piura

This route is really easy and safe. Buses go directly from Loja to Piura and vice-versa (8hrs.), stopping at both Ecuadorian and Peruvian immigracion offices to complete formalities.
From Piura you can go to Mancora on the coast, or continue south to Chiclayo, Trujillo or Lima.
From Loja you can visit Vilcabamba and Zamora, then travel north to Cuenca. From there you can continue north through the Sierra, or West to the Ecuadorian coast.

Zumba - San Ignacio

Travelling to Peru via Zumba is more adventurous and time consuming, but not dificult.
This route is prefered by people visiting the Kuelap ruins & Chachapoyas, an area rich in little explored but magnificent archaeological ruins. It is also an interesting route into the Peruvian Amazon, travelling to Iquitos via Taraota and Yurimaguas.

The Ecuador to Peru route is described, so you'll have to reverse it if coming the other way:

To Chachapoyas (& kuelap)

• Bus: Vilcabamba/Loja to Zumba (4-5hrs)
• Chiva (open sided bus): to La Balsa - Ecuadorian border (2hrs)
• Colectivo: Border to Namballe (15mins) or San Ignacio (2˝hrs)
• Colective/Bus: San Ignacio to Jaen (3˝hrs)
• Bus: Jaen to Pedro Ruiz (4-5hrs)
• Colectivo: Pedro Ruiz to Chachapoyas (2hrs)

To Iquitos

• Bus: Vilcabamba/Loja to Zumba (4-5hrs)
• Chiva (open sided bus): to La Balsa - Ecuadorian border (2hrs)
• Colectivo: Border to Namballe (15mins) or San Ignacio (2˝hrs)
• Colective/Bus: San Ignacio to Jaen (3˝hrs)
• Bus: Jaen to Pedro Ruiz (4-5hrs)
• Bus: Pedro Ruiz to Moyobamba (4hrs) or Tarapoto (6hrs)
• Bus/Colectivo:Tarapota to Yurimaguas (6-10hrs)
• Boat to Iquitos. (2 Days)

Huaquillas - Tumbes

The Ecuadorian immigration office is 4km's before the border
The Peruvian immigration office is 3km's after the border.

• There is transport between Huaquillas (Ecuador) / Tumbes (Peru) and the immigration offices and from there to the border, but Taxi's, porters, money changers and even border guards are all out to rip you off, so beware.
• Cifa & Co-operativa Loja may run a bus directly from Machala to Tumbes, which stops to complete all border formalities. This would be the best option.
• If you have to stay overnight near the border, Machala or Tumbes are the best options.
• If you are travelling to or from Mancora or the Ecuadorian coast, it is as easy to go: Piura, Loja, Cuenca.