This, albeit not being elegant at all, worked for me:

def country_code_converter(input_countries):
    """
    :param input_countries: list containing the name of the countries (can be numpy array)
    :return: list with the ISO alpha 3 codes for the given input ('Unknown Country' if no match found)
    """
    countries = {}
    countries_official = {}
    countries_common = {}

    #loops over all of the countries contained in the pycountry library and populates dictionary
    for country in pycountry.countries:
        countries[country.name] = country.alpha_3

    #loops over the alpha_3 codes from the countries dictionary
    #populates dictionary containing official names and codes
    for alpha_3 in list(countries.values()):
        try:
            countries_official[pycountry.countries.get(alpha_3 = alpha_3).official_name] = alpha_3
        except:
            None
    #same for common names
    for alpha_3 in list(countries.values()):
        try:
            countries_common[pycountry.countries.get(alpha_3 = alpha_3).common_name] = alpha_3
        except:
            None

    codes = []
    # appends ISO codes for all matches by trying different country name types
    # appends Unknown Country if no match found
    for i in input_countries:
        if i in countries.keys():
            codes.append(countries.get(i))

        elif i in countries_official.keys():
            codes.append(countries_official.get(i))

        elif i in countries_common.keys():
            codes.append(countries_common.get(i))

        else:
            codes.append('Unknown Country')
    return codes

You can use this csv file : country code list into a CSV.

import csv

dic = {}
with open("wikipedia-iso-country-codes.csv") as f:
    file= csv.DictReader(f, delimiter=',')
    for line in file:
        dic[line['English short name lower case']] = line['Alpha-2 code']        

countries = ['American Samoa', 'Canada', 'France']

for country in countries:
    print(dic[country])

Will print:

AS
CA
FR

Few more alternatives.