Purpose: Low doses of systemic doxycycline (LD-SD) inhibit angiogenesis and the expression of matrix metalloproteases, which are determinants of pterygium progression. This study aimed to compare the recurrence rate and visual outcome of pterygium excision in patients undergoing chronic treatment with LD-SD for chronic refractory blepharitis and LD-SD-naive patients. Methods: A retrospective analysis of patients that underwent surgical excision and conjunctival graft apposition was conducted. Patients were divided in a TETRA group (under LD-SD treatment at the moment of surgery) and a control group. The main outcome was the rate of recurrence at 1 year postoperatively. Secondary outcomes were the comparisons of surface regularity, visual quality, and dry-eye symptoms at 6-week, 6-month, and 1-year follow-up in the two groups. Results: The TETRA group showed a significantly lower rate of 1-year recurrence both in primary (p = 0.034) and recurrent (p < 0.001) pterygia. The best corrected visual acuity (BCVA), astigmatic error, corneal total root mean square (RMS), and ocular surface disease index (OSDI) significantly reduced during the follow-up in both groups. The surface asymmetry index and high-order aberrations (HOAs) significantly reduced only in the TETRA group. The final BCVA was significantly higher, while the OSDI score and total RMS and HOAs were significantly lower in the TETRA group compared to the control. Conclusions: Patients under treatment with LD-SD showed a lower rate of recurrence at 1-year follow-up compared to controls. These patients also experienced higher BCVA and surface regularity and less dry-eye symptoms.