I've had an interest in the Magellan Circumnavigation as of late, but finding actual primary sources online (besides a French copy of Pigafetta's journal - https://www.wdl.org/en/item/3082/) is extremely hard; I haven't found anything else. No logbooks from the Victoria, none of Andrés de San Martín's navigational notes, none of the other survivors' letters, journals, or depositions, nothing. It's extremely frustrating not to have these, and I thought this would be a great place to ask if anyone has any knowledge or resources as to where I could find these documents.
If not, I'll live, but anything you got would be greatly appreciated.
When Juan Sebastián Elcano made it back to Spain, he was subjected to an interrogation by the officers of the Casa de la Contratación. We have the interrogation's documents, fully digitised by our friends of PARES, link down here.
http://pares.mcu.es/ParesBusquedas20/catalogo/description/122228
If you want more primary sources, our friends at PARES have a whole section for the First Circumnavigation of the World, containing 85 primary sources, including Elcano's interrogation, accounting of the expedition, a full list of the people who died during the journey, reports on the territories visited, a fragmentary log book, etc. Link down here.
http://pares.mcu.es/ParesBusquedas20/catalogo/autoridad/104874
In the National Archive of the Torre do Tombo, in Portugal, there is the "Report on the questions asked to two Spaniards who arrived to Malaca coming from Timor". In there you have the testimony of Martín de Ayamonte, who defected from the Victoria ship, and eventually made it to Portugal, where he was held prisoner. I also provide a link for this.
https://digitarq.arquivos.pt/details?id=3801974
A translation into Spanish can be found here:
http://www.memoriachilena.gob.cl/602/w3-article-122051.html
And a more recent one, with notes, is available here:
Edit: I entirely forgot to add Martín Fernández de Navarrete's Colección de viages y descubrimientos, volume IV, that contains transcriptions of primary sources regarding Magallanes and Elcano's voyage.
I hope these links will be helpful to you