September is a busy time in Venice. The Art Biennale should still be running, and for the last two years there's been Glass Week in the second half of the month. I think there's a regatta at some point as well.
Although I'd choose Venice over Padua, I like Padua a lot. These are the sightseeing options I laid out before my most recent trip to Padua (3 nights in September 2022):
Scrovegni Chapel: Buy ticket a few days ahead. There's a combo ticket including Musei Civici agli Eremitani and Palazzo Zuckermann.
Palazzo Zuckemann: Applied and decorative art 16C-17C, including ceramics, plus impressionist paintings.
Musei Civici agli Eremitani: Former monastery with excellent 13C-18C Venetian art and archaeological collection (including Egyptian); no English text for archeological material. Cloister gardens with ancient archaeological fragments and modern sculptures.
Chiesa degli Eremitani: Built 1276-1306; magnificent roof, wall tombs and 15C Mantegna frescoes (substantially damaged during WWII Allied bombing).
Museo del Risorgimento, upstairs at Caffe Pedrocchi (Galleria Pedrocchi 11), Via Cavour/Piazzetta Cappellato Pedrocchi: Propaganda posters and interesting 30-min film. Covers period 1797-1848. English-accessible. I haven't been here and am not sure it's still open.
Palazzo Bo’, Via VIII Febbraio 7: 16C Renaissance palazzo, now part of university. Two beautiful old courtyards (open; entered under “Gymnasium” inscription). Frescoed stairway off second courtyard. Interior, including anatomy theatre, accessible only with 45-min. tour (English usually around midday Mon-Sat). I haven't taken the tour.
Palazzo della Ragione, Piazza delle Erbe: Early 13C Gothic with frescoed (15C. after fire) Great Hall. Sometimes used for art exhibitions. Large Indoor market ground floor with produce, bread, cheese, prepared foods.
Jewish Quarter, opposite Palazzo della Ragione (Piazza delle Erbe side): Charming area of arcaded lanes. Via dell’Arco, Via delle Piazze and Via San Martino e Solerino.
Museo Diocesano, Palazzo Vescovile.
Cattedrale di Santa Maria Assunta (Duomo), Piazza del Duomo: Main points of interest are Vangi’s contemporary crucifix and sculptures. RS says skippable.
Battistero di San Giovanni Battista, Pza del Duomo: 13C Romanesque; Byzantine-influenced Menabuoi frescoes.
Palazzo del Capitanio: Astronomical clock. On Piazza dei Signori (15C-16C buildings). Morning clothing market.
MUSME (Museo di Storia della Medicina): Padua’s contribution to world medicine 16C-19C. I haven't been here.
Statue of Gattamelata, Piazza del Santo (outside Basilica): Great Renaissance work by Donatello.
Basilica di Sant’Antonio (Il Santo): Beautiful Capella delle Reliquie/Capella del Santo (1245-1430). Nine fine marble reliefs (Donatello?) near tomb. Three cloisters. Many pilgrims. Many masses. Church itself is free.
- Basilica Complex includes multiple buildings with entry fees: Oratorio di San Giorgio, Scoletta (Scuola) del Santo (has some Titians), Museo Antoniano (works by Mantegna, Tiepolo and Carpaccio),
Museo della Devozione Popolare (votives and folk art).
Botanical garden.