Quick answer
Two different jobs
Évora's job is to be seen. It has been the region's showpiece for centuries — a university, a Roman temple standing in the middle of town, a cathedral, a bone chapel, streets of azulejos and wrought iron that earned World Heritage status in 1986. It does that job superbly, and the world has noticed: coach parties from Lisbon, tour groups at the temple by 11:00, menus in four languages.
Beja's job is to run the Baixo Alentejo. It is a market and administrative capital on a low hill in the wheat plain, and it does not perform for visitors — which is exactly its charm. The old town is compact and whitewashed, the castle keep is the tallest in Portugal, the convent tied to the seventeenth-century Portuguese Letters sits in an ordinary neighbourhood, and at dusk the Praça da República belongs to the town, not to the tour schedule.
Sights, honestly compared
On monuments alone, Évora wins on volume and fame: temple, cathedral, chapel of bones, aqueduct, and a dense historic centre where something remarkable waits on every second corner. Beja answers with fewer, quieter cards: the castle and its keep with the plain running flat to the horizon, Roman Pax Julia visible under the streets at the Rua do Sembrano, the Convento da Conceição's story, and the Sé at the top of town. If you measure a visit in photographs, Évora fills more of them. If you measure it in unhurried attention per sight, Beja gives you room Évora no longer can.
Crowds, cost and pace
Évora in season means booking restaurants, queuing for the chapel, and sharing the streets. Beja means walking into a lunch house at 12:45 and finding a table — usually. Accommodation and meals run noticeably cheaper in Beja, and the pace is the region's own: slow mornings, serious lunches, dead afternoons in summer heat, and towns that come back to life at dusk. Our morning walking route and eating list are built around exactly that rhythm.
Getting there
From Lisbon, Évora is the easier trip: about 130 km, with frequent trains taking around an hour and a half. Beja is deeper in — around 180 km, with direct trains and buses that run less often, so check times in both directions. Between the two towns it is a drive of a little over an hour through open country. That geography explains the crowds as much as the monuments do.
The itinerary that uses both
The best Alentejo plan is not a choice but a sequence: Évora first for the set pieces, then south to Beja to sleep where the region is quieter and cheaper, with Mértola and the Guadiana waiting below it. Two or three nights, one region, both arguments heard.