Pre-slaughter handling of pigs has been documented to affect the quality of meat though no studies have investigated this relationship in the Kenyan context. This study aimed to determine the prevalence of gross lesions and practices related to sub-optimal welfare in pigs presented for slaughter while analyzing the relationship between occurrence of these lesions and meat quality. A cross-sectional study was conducted at a medium scale, non-integrated pig abattoir supplying to the Nairobi market, with a capacity to slaughter approximately 40 pigs a day. Data on welfare-associated lesions and handling practices were obtained from 529 pig carcasses and traders respectively. 387 pork samples were collected, and their quality evaluated by measuring their pH, meat color and drip loss. These three parameters were used to classify pork into four recognized categories namely: Red, Firm, Non-exudative (RFN), Pale Soft Exudative (PSE), Dark Firm Dry (DFD) and Red Soft Exudative (RSE). Almost all pigs were inefficiently stunned as evidenced by the presence of consciousness post-stunning. The majority of pigs (82.97%) having one or more welfare-associated gross lesions. Other animal welfare malpractices observed were high loading density and inadequate rest periods between transport and slaughter. A quarter of the pork samples were of sub-optimal quality including: RSE (11.36%), PSE (2.58%) and DFD (2.58%). Multinomial logistic regression revealed that pork originating from pigs transported at a high loading density had increased odds of being classified as DFD (OR 13.41, 95% CI 2.59–69.46). The findings indicate the need to educate stakeholders in the pork value chains on improved pig handling before and during slaughter to enhance pig welfare pre-slaughter and pork quality post-slaughter. Animal welfare legislation enforcement and implementation was observed to be insufficient. There is a need to educate key stakeholders on its importance of being put into practice both from economic and welfare perspectives.