Quality changes due to oven-baking of sardine for 20, 40, 50 and 60 min and due to deep frying of anchovy for 2, 3, 4 and 5 min in olive and sunflower oil were studied. Linear increase in total losses with the time of processing was observed. A linear inverse relationship was observed between moisture/lipid and moisture/protein due to time of baking of sardines and time of frying of anchovies (wet matter). However, no changes were detected in sardine samples due to time of baking (dry matter), while a reduction in proteins and ash followed by an increase in lipids was detected in fried anchovies due to time of frying (dry matter). The fatty acid profiles indicated that a rich in EPA + DHA (33.16%) and in ω-3/ω-6 ratio (9.40) baked sardines can be produced in 20 min at 200 °C. The fatty acid profiles of fried anchovies tremendously changed, indicating entirely different products. Olive oil is probably a better medium to fry fish products, since either the two beneficial fatty acids (EPA and DHA) detected at higher concentrations in anchovies fried in olive oil or the ω-3/ω-6 ratio remained at higher values (0.71-2.56). An increase of cholesterol and squalene content with increasing the time of baking was detected in sardine samples, probably due to decline of moisture content. On the contrary, cholesterol significantly reduced due to frying of anchovy in olive oil. Simultaneously squalene concentration significantly and linearly increased, from 3.87 mg/100 g in the unprocessed anchovies to 73.25 mg/100 g in the samples fried for 5 min, indicating its existence at beneficial levels, besides low cholesterol concentration detected in fried olive oil and squalene concentration gradually and linearly decreased, confirming the absorption from the anchovy samples. Similar was the changes of cholesterol and squalene in anchovies samples fried in sunflower oil.