You will usually eat at home. If you are the master (i.e., the master craftsman, owner and manager of the business), you own the building. If you are an apprentice, or an employed journeyman, you not only work in the master's workshop, you live in the master's home. A common house plan was for the workshop to be on the ground floor, the master's family's living quarters on the floor above (the 1st floor, for those who count ground-1st-2nd), and the apprentices (and journeymen, if any) on the top floor above that (the 2nd floor). There might be a cellar for storage.
Details beyond this would depend somewhat on the trade. One common pattern was for the front part of the ground floor (fronting the street) to be the workshop and the retail space, with a hall to the rear. This hall would be where lunch would be eaten, the master and his family, the apprentices, and the employees eating together. If there is a courtyard, and the weather is suitable, you might eat in the courtyard. If more separation is wanted between the workshop and the retail space, then there might be separate rooms for workshop and retail, with the retail space on the street frontage. Alternatively, a semi-permanent retail booth might be built in the street in front of the building (and such booths might be built in front of pure residences, or workshops that don't require such a booth, to be rented to retailers).
Some trades need more space, and were often segregated, clustered together in districts. Butchers, blacksmiths, tanners, and other trades generating lots of noise, smoke, or stench would typically be segregated. Butchers, for example, would often have large yards behind the house, used for keeping livestock prior to slaughter, and slaughtering and the first stages of butchering would take place in the yard. Butchers often had a retail booth in the street in front of the house.
Thus, the standard lunch for a skilled craftsman was a substantial home-cooked lunch (typically the biggest meal of the day). Just lock the front door or booth, retire to the hall behind the workshop, and eat (and maybe nap), and then start work again in the afternoon.
There were variation on this pattern. Workers who worked alone (and often lived alone) might rent a small workshop. This might have simple living quarters above, or living quarters could be rented nearby. Often without significant cooking facilities in either their small workshop or smaller living space, and without family to cook for them while they work in the morning, these craftsmen might choose to eat out, to buy their lunch. Traders selling from booths in the market might also buy their lunch, and unskilled labourers, too. Their other choice would be to lock up their market booth for lunch, and go home and eat. Their choice would depend on whether they lived alone, or with their family or employer.
This pattern of lunch being the main meal, and being eaten at home, continued in many places in Europe well into the Industrial Age. Separate work and living places only became the normal situation with industrialisation, and it took time for dining habits to catch up with the new work and living habits. Intermediate between the ancient pattern of workers eating a main-meal lunch at home and the modern pattern of workers bringing a small-meal lunch with them, or buying lunch, was a substantial home-cooked lunch being delivered to the worker. In some places, a delivered home-cooked meal is still common, e.g., in Mumbai, where they are often delivered by professional tiffin-carriers: https://en.wikipedia.org/wiki/File:Mumbai_Dabbawala_or_Tiffin_Wallahs-_200,000_Tiffin_Boxes_Delivered_Per_Day.jpg
References and further reading:
Residential and workplace patterns:
Langton, J. (1975), "Residential Patterns in Pre-Industrial Cities: Some Case Studies from Seventeenth-Century Britain", Transactions of the Institute of British Geographers 65, 1-27. https://doi.org/10.2307/621607 https://www.jstor.org/stable/621607
Sjoberg, G. (1955), "The Preindustrial City", American Journal of Sociology 60(5), 438-445. https://www.jstor.org/stable/2772531
Medieval house/workshop plans:
W. A. Pantin (1962), "Medieval English Town-House Plans", Medieval Archaeology 6:1, 202-239. https://doi.org/10.1080/00766097.1962.11735667 https://www.semanticscholar.org/paper/Medieval-English-Town-House-Plans-Pantin/c2e255967c3459248d09d6e4d11af680b85f85f1
Clark, D. (2000), "The Shop within?: An Analysis of the Architectural Evidence for Medieval Shops", Architectural History 43, 58-87. https://doi.org/10.2307/1568686 https://www.jstor.org/stable/1568686
Food and dining patterns, and changes with industrialisation: